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Intermittent "not a valid binary" error during package install #655

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Jondeen opened this issue Jun 27, 2024 · 12 comments
Open

Intermittent "not a valid binary" error during package install #655

Jondeen opened this issue Jun 27, 2024 · 12 comments

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@Jondeen
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Jondeen commented Jun 27, 2024 •
edited
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Hi,

I'm experiencing an intermittent error installing a packge using pak. It does not happen every time, but pretty close to 90% of the times I try.

The error seems to relate to #467 .

I'm building in a Docker file, and the package in question ([email protected]) does not install successfully, using R4.3.2 and default install.packages('pak'):

133.6 Error:
133.6 ! error in pak subprocess
133.6 Caused by error in `verify_extracted_package(filename, pkg_cache)`:
133.6 !
133.6 '/tmp/RtmpfQ56b7/file34716455fa/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.3/reshape2_1.4.4.tar.gz'
133.6 is not a valid binary, it is missing reshape2/Meta/package.rds.
133.6 ---
133.6 Backtrace:
133.6 1. pak::pak(packages)
133.6 2. pak::pkg_install(pkg, ...)
133.6 3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
133.6 4. err$throw(res$error)
133.6 ---
133.6 Subprocess backtrace:
133.6  1. base::withCallingHandlers(cli_message = function(msg) { …
133.6  2. get("pkg_install_do_plan", asNamespace("pak"))(...)
133.6  3. proposal$install()
133.6  4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
133.6  5. base::withCallingHandlers({ …
133.6  6. pkgdepends:::handle_events(state, events)
133.6  7. pkgdepends:::handle_event(state, i)
133.6  8. proc$get_result()
133.6  9. processx:::process_get_result(self, private)
133.6 10. private$post_process()
133.6 11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
133.6 12. pkgdepends:::verify_extracted_package(filename, pkg_cache)
133.6 13. base::throw(pkg_error("{.path {filename}} is not a valid binary, it is missing {…
133.6 14. | base::signalCondition(cond)
133.6 15. global (function (e) …
133.6 Execution halted

The package is quite small, and I wonder if there could be a r/w race condition causing it. Installing it using install.packages works fine every time.

Let me know if I can contribute with other details.
@gaborcsardi
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Can you show a reproducible example and/or the full output of the installation?

@Jondeen
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Jondeen commented Jun 28, 2024 •
edited
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Of course! Here you go:

This setup is from WSL, but I see the same happen on Docker hub build infrastructure.

Adding reshape2 to be installed using install.packages first resolves the issue. reshape2 is currently being pulled in as a dependency, but adding it to the list of packages to be installed by itself generates the same error.

Dockerfile

FROM rocker/rstudio:4.3.2
RUN R -e 'install.packages(c("pak","pkgdepends"), repos = "https://cloud.r-project.org")'
COPY stage_1_packages.txt /tmp/
RUN R -e "packages <- readLines('/tmp/stage_1_packages.txt'); pak::pak(packages); pak::cache_clean()"

stage_1_packages.txt

stats4
grid
stats
graphics
grDevices
utils
datasets
methods
base
stringr
gridExtra
GSA
ggforce
ggfortify
ggplotify
cowplot
corrplot
fgsea
dplyr
readxl
tximeta
vsn
tximport
sva
BiocParallel
mgcv
nlme
rhdf5
RColorBrewer
pheatmap
org.Hs.eg.db
org.Mm.eg.db
limma
IHW
GSEABase
graph
annotate
XML
AnnotationDbi
ggpubr
genefilter
DOSE
DESeq2
SummarizedExperiment
Biobase
MatrixGenerics
matrixStats
GenomicRanges
GenomeInfoDb
IRanges
S4Vectors
BiocGenerics
ComplexHeatmap
clusterProfiler
biomaRt
haven
VennDiagram
futile.logger
tidyr
scales
plotly
patchwork
openxlsx
Hmisc
hexbin
gplots
ggrepel
ggbeeswarm
factoextra
ggplot2
apeglm
IRkernel
MarieOestreich/hCoCena/hCoCena-r-package

Output

docker build .
[+] Building 0.0s (0/0)                                                                                                                                                                                                                                                                            docker:home
[+] Building 217.1s (8/11)                                                                                                                                                                                                                                                                         docker:home
 => [internal] load build definition from Dockerfile                                                                                                                                                                                                                                                      0.4s
 => => transferring dockerfile: 1.75kB                                                                                                                                                                                                                                                                    0.1s
 => [internal] load .dockerignore                                                                                                                                                                                                                                                                         0.4s
 => => transferring context: 2B                                                                                                                                                                                                                                                                           0.1s
 => [internal] load metadata for docker.io/rocker/rstudio:4.3.2                                                                                                                                                                                                                                           2.7s
 => [internal] load build context                                                                                                                                                                                                                                                                         0.2s
 => => transferring context: 723B                                                                                                                                                                                                                                                                         0.2s
 => CACHED [1/7] FROM docker.io/rocker/rstudio:4.3.2@sha256:2f48314dfffab8ac2e1bc1797b0564b1f96927f702c064ab2cc69ce1b1c62016                                                                                                                                                                              0.0s
 => [2/7] RUN R -e 'install.packages(c("pak","pkgdepends"), repos = "https://cloud.r-project.org")'                                                                                                                                                                                                     111.0s
 => [3/7] COPY stage_1_packages.txt /tmp/                                                                                                                                                                                                                                                                 0.0s
 => ERROR [4/7] RUN R -e "packages <- readLines('/tmp/stage_1_packages.txt'); pak::pak(packages); pak::cache_clean()"                                                                                                                                                                                   102.9s
------                                                                                                                                                                                                                                                                                                         
 > [4/7] RUN R -e "packages <- readLines('/tmp/stage_1_packages.txt'); pak::pak(packages); pak::cache_clean()":                                                                                                                                                                                                
0.496                                                                                                                                                                                                                                                                                                          
0.496 R version 4.3.2 (2023-10-31) -- "Eye Holes"                                                                                                                                                                                                                                                              
0.496 Copyright (C) 2023 The R Foundation for Statistical Computing                                                                                                                                                                                                                                            
0.496 Platform: x86_64-pc-linux-gnu (64-bit)                                                                                                                                                                                                                                                                   
0.496 
0.496 R is free software and comes with ABSOLUTELY NO WARRANTY.
0.496 You are welcome to redistribute it under certain conditions.
0.496 Type 'license()' or 'licence()' for distribution details.
0.496 
0.496   Natural language support but running in an English locale
0.496 
0.496 R is a collaborative project with many contributors.
0.496 Type 'contributors()' for more information and
0.496 'citation()' on how to cite R or R packages in publications.
0.496 
0.496 Type 'demo()' for some demos, 'help()' for on-line help, or
0.496 'help.start()' for an HTML browser interface to help.
0.496 Type 'q()' to quit R.
0.496 
0.566 > packages <- readLines('/tmp/stage_1_packages.txt'); pak::pak(packages); pak::cache_clean()
1.826 ! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
1.898 
4.060 ✔ Updated metadata database: 3.66 MB in 9 files.
4.061 
4.066 ℹ Updating metadata database
6.948 ✔ Updating metadata database ... done
6.949 
11.26  
11.27 → Will install 289 packages.
11.28 → Will update 2 packages.
11.28 → Will download 1 CRAN package (15.03 kB).
11.29 → Will download 290 packages with unknown size.
11.31 + abind                            1.4-5       [dl]
11.31 + affy                             1.80.0      [bld][cmp][dl]
11.31 + affyio                           1.72.0      [bld][cmp][dl]
11.31 + annotate                         1.80.0      [bld][dl]
11.31 + AnnotationDbi                    1.64.1      [bld][dl]
11.31 + AnnotationFilter                 1.26.0      [bld][dl]
11.31 + AnnotationHub                    3.10.1      [bld][cmp][dl]
11.31 + ape                              5.7-1       [dl]
11.31 + apeglm                           1.24.0      [bld][cmp][dl]
11.31 + aplot                            0.2.2       [dl]
11.31 + askpass                          1.2.0       [dl]
11.31 + assertthat                       0.2.1       [dl]
11.31 + backports                        1.4.1       [dl]
11.31 + base64enc                        0.1-3       [dl]
11.31 + base64url                        1.4         [dl]
11.31 + bbmle                            1.0.25.1    [dl]
11.31 + bdsmatrix                        1.3-6       [dl]
11.31 + beeswarm                         0.4.0       [dl]
11.31 + BH                               1.84.0-0    [dl]
11.31 + Biobase                          2.62.0      [bld][cmp][dl]
11.31 + BiocFileCache                    2.10.2      [bld][dl]
11.31 + BiocGenerics                     0.48.1      [bld][dl]
11.31 + BiocIO                           1.12.0      [bld][dl]
11.31 + BiocManager                      1.30.22     [dl]
11.31 + BiocParallel                     1.36.0      [bld][cmp][dl]
11.31 + BiocVersion                      3.18.1      [bld][dl]
11.31 + biomaRt                          2.58.2      [bld][dl]
11.31 + Biostrings                       2.70.3      [bld][cmp][dl]
11.31 + bit                              4.0.5       [dl]
11.31 + bit64                            4.0.5       [dl]
11.31 + bitops                           1.0-7       [dl]
11.31 + blob                             1.2.4       [dl]
11.31 + broom                            1.0.5       [dl]
11.31 + bslib                            0.6.1       [dl]
11.31 + cachem                           1.0.8       [dl]
11.31 + Cairo                            1.6-2       [dl] + ✖ libcairo2-dev
11.31 + car                              3.1-2       [dl]
11.31 + carData                          3.0-5       [dl]
11.31 + caTools                          1.18.2      [dl]
11.31 + cellranger                       1.1.0       [dl]
11.31 + checkmate                        2.3.1       [dl]
11.31 + circlize                         0.4.16      [dl]
11.31 + clipr                            0.8.0       [dl]
11.31 + clue                             0.3-65      [dl]
11.31 + clusterProfiler                  4.10.1      [bld][dl]
11.31 + coda                             0.19-4.1    [dl]
11.31 + colorspace                       2.1-0       [dl]
11.31 + combinat                         0.0-8       [dl]
11.31 + commonmark                       1.9.1       [dl]
11.31 + ComplexHeatmap                   2.18.0      [bld][dl]
11.31 + corrplot                         0.92        [dl]
11.31 + cowplot                          1.1.3       [dl]
11.31 + cpp11                            0.4.7       [dl]
11.31 + crayon                           1.5.2       [dl]
11.31 + crosstalk                        1.2.1       [dl]
11.31 + data.table                       1.15.0      [dl]
11.31 + DBI                              1.2.2       [dl]
11.31 + dbplyr                           2.4.0       [dl]
11.31 + DelayedArray                     0.28.0      [bld][cmp][dl]
11.31 + dendextend                       1.17.1      [dl]
11.31 + DESeq2                           1.42.1      [bld][cmp][dl]
11.31 + digest                           0.6.34      [dl]
11.31 + doParallel                       1.0.17      [dl]
11.31 + DOSE                             3.28.2      [bld][dl]
11.31 + downloader                       0.4         [dl]
11.31 + dplyr                            1.1.4       [dl]
11.31 + DT                               0.32        [dl]
11.31 + edgeR                            4.0.16      [bld][cmp][dl]
11.31 + egg                              0.4.5       [dl]
11.31 + ellipse                          0.5.0       [dl]
11.31 + ellipsis                         0.3.2       [dl]
11.31 + emdbook                          1.3.13      [dl]
11.31 + emmeans                          1.10.0      [dl]
11.31 + enrichplot                       1.22.0      [bld][dl]
11.31 + ensembldb                        2.26.0      [bld][dl]
11.31 + estimability                     1.5         [dl]
11.31 + evaluate                         0.23        [dl]
11.31 + factoextra                       1.0.7       [dl]
11.31 + FactoMineR                       2.9         [dl]
11.31 + fansi                            1.0.6       [dl]
11.31 + farver                           2.1.1       [dl]
11.31 + fastmap                          1.1.1       [dl]
11.31 + fastmatch                        1.1-4       [dl]
11.31 + fdrtool                          1.2.17      [dl]
11.31 + fgsea                            1.28.0      [bld][cmp][dl]
11.31 + flashClust                       1.01-2      [dl]
11.31 + FNN                              1.1.4       [dl]
11.31 + fontawesome                      0.5.2       [dl]
11.31 + forcats                          1.0.0       [dl]
11.31 + foreach                          1.5.2       [dl]
11.31 + formatR                          1.14        [dl]
11.31 + Formula                          1.2-5       [dl]
11.31 + fs                               1.6.3       [dl] + ✔ make
11.31 + futile.logger                    1.4.3       [dl]
11.31 + futile.options                   1.0.1       [dl]
11.31 + genefilter                       1.84.0      [bld][cmp][dl]
11.31 + generics                         0.1.3       [dl]
11.31 + GenomeInfoDb                     1.38.8      [bld][dl]
11.31 + GenomeInfoDbData                 1.2.11      [bld][dl]
11.31 + GenomicAlignments                1.38.2      [bld][cmp][dl]
11.31 + GenomicFeatures                  1.54.4      [bld][dl]
11.31 + GenomicRanges                    1.54.1      [bld][cmp][dl]
11.31 + GetoptLong                       1.0.5       [dl] + ✔ perl
11.31 + ggbeeswarm                       0.7.2       [dl]
11.31 + ggforce                          0.4.2       [dl]
11.31 + ggfortify                        0.4.16      [dl]
11.31 + ggfun                            0.1.4       [dl]
11.31 + ggnewscale                       0.4.10      [dl]
11.31 + ggplot2                          3.5.0       [dl]
11.31 + ggplotify                        0.1.2       [dl]
11.31 + ggpubr                           0.6.0       [dl]
11.31 + ggraph                           2.2.0       [dl]
11.31 + ggrepel                          0.9.5       [dl]
11.31 + ggsci                            3.0.0       [dl]
11.31 + ggsignif                         0.6.4       [dl]
11.31 + ggtree                           3.10.1      [bld][dl]
11.31 + GlobalOptions                    0.1.2       [dl]
11.31 + glpkAPI                          1.3.4       [dl] + ✖ libglpk-dev
11.31 + glue                             1.7.0       [dl]
11.31 + GO.db                            3.18.0      [bld][dl]
11.31 + GOSemSim                         2.28.1      [bld][cmp][dl]
11.31 + gplots                           3.1.3.1     [dl]
11.31 + graph                            1.80.0      [bld][cmp][dl]
11.31 + graphlayouts                     1.1.0       [dl]
11.31 + gridExtra                        2.3         [dl]
11.31 + gridGraphics                     0.5-1       [dl]
11.31 + GSA                              1.03.2      [dl]
11.31 + GSEABase                         1.64.0      [bld][dl]
11.31 + gson                             0.1.0       [dl]
11.31 + gtable                           0.3.4       [dl]
11.31 + gtools                           3.9.5       [dl]
11.31 + haven                            2.5.4       [dl] + ✔ make, ✖ zlib1g-dev
11.31 + hcocena                          1.1.1       [bld][cmp][dl] (GitHub: 0ffd2f2)
11.31 + HDO.db                           0.99.1      [bld][dl]
11.31 + hexbin                           1.28.3      [dl]
11.31 + highr                            0.10        [dl]
11.31 + Hmisc                            5.1-1       [dl]
11.31 + hms                              1.1.3       [dl]
11.31 + htmlTable                        2.4.2       [dl]
11.31 + htmltools                        0.5.7       [dl]
11.31 + htmlwidgets                      1.6.4       [dl]
11.31 + httpuv                           1.6.14      [dl] + ✔ make, ✖ zlib1g-dev
11.31 + httr                             1.4.7       [dl]
11.31 + igraph                           2.0.2       [dl] + ✖ libglpk-dev, ✖ libxml2-dev
11.31 + IHW                              1.30.0      [bld][dl]
11.31 + interactiveDisplayBase           1.40.0      [bld][dl]
11.31 + IRanges                          2.36.0      [bld][cmp][dl]
11.31 + IRdisplay                        1.1         [dl]
11.31 + IRkernel                         1.3.2       [dl] + ✔ python3
11.31 + irlba                            2.3.5.1     [dl]
11.31 + isoband                          0.2.7       [dl]
11.31 + iterators                        1.0.14      [dl]
11.31 + jquerylib                        0.1.4       [dl]
11.31 + KEGGREST                         1.42.0      [bld][dl]
11.31 + knitr                            1.45        [dl] + ✖ pandoc
11.31 + labeling                         0.4.3       [dl]
11.31 + lambda.r                         1.2.4       [dl]
11.31 + later                            1.3.2       [dl]
11.31 + lazyeval                         0.2.2       [dl]
11.31 + leaps                            3.1         [dl]
11.31 + leidenAlg                        1.1.3       [dl] + ✖ libglpk-dev, ✔ make, ✖ libxml2-dev
11.31 + leidenbase                       0.1.27      [dl]
11.31 + lifecycle                        1.0.4       [dl]
11.31 + limma                            3.58.1      [bld][cmp][dl]
11.31 + lme4                             1.1-35.1    [dl]
11.31 + locfit                           1.5-9.8     [dl]
11.31 + lpsymphony                       1.30.0      [bld][cmp][dl] + ✔ make
11.31 + magrittr                         2.0.3       [dl]
11.31 + MatrixGenerics                   1.14.0      [bld][dl]
11.31 + MatrixModels                     0.5-3       [dl]
11.31 + matrixStats                      1.2.0       [dl]
11.31 + MCDA                             0.1.0       [dl]
11.31 + memoise                          2.0.1       [dl]
11.31 + mgcv                   1.9-0   → 1.9-1       [dl]
11.31 + mime                             0.12        [dl]
11.31 + minqa                            1.2.6       [dl] + ✔ make
11.31 + multcompView                     0.1-9       [dl]
11.31 + munsell                          0.5.0       [dl]
11.31 + mvtnorm                          1.2-4       [dl]
11.31 + networkD3                        0.4         [dl]
11.31 + nlme                   3.1-163 → 3.1-164     [dl]
11.31 + nloptr                           2.0.3       [dl] + ✖ cmake
11.31 + numDeriv                         2016.8-1.1  [dl]
11.31 + openssl                          2.1.1       [dl] + ✔ libssl-dev
11.31 + openxlsx                         4.2.5.2     [dl]
11.31 + org.Hs.eg.db                     3.18.0      [bld][dl]
11.31 + org.Mm.eg.db                     3.18.0      [bld][dl]
11.31 + patchwork                        1.2.0       [dl]
11.31 + pbdZMQ                           0.3-11      [dl] + ✖ libzmq3-dev
11.31 + pbkrtest                         0.5.2       [dl]
11.31 + pbmcapply                        1.5.1       [dl]
11.31 + pheatmap                         1.0.12      [dl]
11.31 + pillar                           1.9.0       [dl]
11.31 + pkgconfig                        2.0.3       [dl]
11.31 + plotly                           4.10.4      [dl]
11.31 + plyr                             1.8.9       [dl]
11.31 + png                              0.1-8       [dl] + ✖ libpng-dev
11.31 + polyclip                         1.10-6      [dl]
11.31 + polynom                          1.4-1       [dl]
11.31 + preprocessCore                   1.64.0      [bld][cmp][dl]
11.31 + prettyunits                      1.2.0       [dl]
11.31 + pROC                             1.18.5      [dl]
11.31 + progress                         1.2.3       [dl]
11.31 + promises                         1.2.1       [dl]
11.31 + ProtGenerics                     1.34.0      [bld][dl]
11.31 + purrr                            1.0.2       [dl]
11.31 + quantreg                         5.97        [dl]
11.31 + qvalue                           2.34.0      [bld][dl]
11.31 + rappdirs                         0.3.3       [dl]
11.31 + RColorBrewer                     1.1-3       [dl]
11.31 + Rcpp                             1.0.12      [dl]
11.31 + RcppAnnoy                        0.0.22      [dl]
11.31 + RcppArmadillo                    0.12.8.0.0  [dl]
11.31 + RcppEigen                        0.3.3.9.4   [dl]
11.31 + RcppNumerical                    0.6-0       [dl]
11.31 + RCurl                            1.98-1.14   [dl] + ✔ make, ✔ libcurl4-openssl-dev
11.31 + RCy3                             2.22.1      [bld][dl]
11.31 + readr                            2.1.5       [dl]
11.31 + readxl                           1.4.3       [dl]
11.31 + rematch                          2.0.0       [dl]
11.31 + repr                             1.1.6       [dl]
11.31 + reshape2                         1.4.4       [dl]
11.31 + restfulr                         0.0.15      [bld][cmp][dl] (15.03 kB)
11.31 + Rglpk                            0.6-5.1     [dl] + ✖ libglpk-dev
11.31 + rhdf5                            2.46.1      [bld][cmp][dl] + ✔ make
11.31 + rhdf5filters                     1.14.1      [bld][cmp][dl] + ✔ make
11.31 + Rhdf5lib                         1.24.2      [bld][cmp][dl] + ✔ make
11.31 + Rhtslib                          2.4.1       [bld][cmp][dl] + ✔ libcurl4-openssl-dev
11.31 + rjson                            0.2.21      [dl]
11.31 + RJSONIO                          1.3-1.9     [dl]
11.31 + rlang                            1.1.3       [dl]
11.31 + rlist                            0.4.6.2     [dl]
11.31 + rmarkdown                        2.25        [dl] + ✖ pandoc
11.31 + Rsamtools                        2.18.0      [bld][cmp][dl] + ✔ make
11.31 + RSQLite                          2.3.5       [dl]
11.31 + rstatix                          0.7.2       [dl]
11.31 + rstudioapi                       0.15.0      [dl]
11.31 + rtracklayer                      1.62.0      [bld][cmp][dl]
11.31 + S4Arrays                         1.2.1       [bld][cmp][dl]
11.31 + S4Vectors                        0.40.2      [bld][cmp][dl]
11.31 + sass                             0.4.8       [dl] + ✔ make
11.31 + scales                           1.3.0       [dl]
11.31 + scatterpie                       0.2.1       [dl]
11.31 + scatterplot3d                    0.3-44      [dl]
11.31 + sccore                           1.0.5       [dl]
11.31 + shadowtext                       0.1.3       [dl]
11.31 + shape                            1.4.6.1     [dl]
11.31 + shiny                            1.8.0       [dl]
11.31 + slam                             0.1-50      [dl]
11.31 + snow                             0.4-4       [dl]
11.31 + sourcetools                      0.1.7-1     [dl]
11.31 + SparseArray                      1.2.4       [bld][cmp][dl]
11.31 + SparseM                          1.81        [dl]
11.31 + statmod                          1.5.0       [dl]
11.31 + stringi                          1.8.3       [dl] + ✖ libicu-dev
11.31 + stringr                          1.5.1       [dl]
11.31 + SummarizedExperiment             1.32.0      [bld][dl]
11.31 + sva                              3.50.0      [bld][cmp][dl]
11.31 + sys                              3.4.2       [dl]
11.31 + systemfonts                      1.0.5       [dl] + ✖ libfontconfig1-dev, ✖ libfreetype6-dev
11.31 + tibble                           3.2.1       [dl]
11.31 + tidygraph                        1.3.1       [dl]
11.31 + tidyr                            1.3.1       [dl]
11.31 + tidyselect                       1.2.0       [dl]
11.31 + tidytree                         0.4.6       [dl]
11.31 + tinytex                          0.49        [dl]
11.31 + treeio                           1.26.0      [bld][dl]
11.31 + triangle                         1.0         [dl]
11.31 + tweenr                           2.0.3       [dl]
11.31 + tximeta                          1.20.3      [bld][dl]
11.31 + tximport                         1.30.0      [bld][dl]
11.31 + tzdb                             0.4.0       [dl]
11.31 + utf8                             1.2.4       [dl]
11.31 + uuid                             1.2-0       [dl]
11.31 + uwot                             0.1.16      [dl]
11.31 + vctrs                            0.6.5       [dl]
11.31 + VennDiagram                      1.7.3       [dl]
11.31 + vipor                            0.4.7       [dl]
11.31 + viridis                          0.6.5       [dl]
11.31 + viridisLite                      0.4.2       [dl]
11.31 + vroom                            1.6.5       [dl]
11.31 + vsn                              3.70.0      [bld][cmp][dl]
11.31 + withr                            3.0.0       [dl]
11.31 + xfun                             0.42        [dl]
11.31 + XML                              3.99-0.16.1 [dl] + ✖ libxml2-dev
11.31 + xml2                             1.3.6       [dl] + ✖ libxml2-dev
11.31 + xtable                           1.8-4       [dl]
11.31 + XVector                          0.42.0      [bld][cmp][dl]
11.31 + yaml                             2.3.8       [dl]
11.31 + yulab.utils                      0.1.4       [dl]
11.31 + zlibbioc                         1.48.2      [bld][cmp][dl]
11.32 → Will install 11 system packages:
11.32 + cmake               - nloptr                           
11.32 + libcairo2-dev       - Cairo                            
11.32 + libfontconfig1-dev  - systemfonts                      
11.32 + libfreetype6-dev    - systemfonts                      
11.32 + libglpk-dev         - igraph, glpkAPI, leidenAlg, Rglpk
11.32 + libicu-dev          - stringi                          
11.32 + libpng-dev          - png                              
11.32 + libxml2-dev         - xml2, XML, igraph, leidenAlg     
11.32 + libzmq3-dev         - pbdZMQ                           
11.32 + pandoc              - knitr, rmarkdown                 
11.32 + zlib1g-dev          - httpuv, haven                    
11.48 ℹ Getting 1 pkg (15.03 kB) and 290 pkgs with unknown sizes
15.56 ✔ Got glue 1.7.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (150.25 kB)
15.58 ✔ Got lifecycle 1.0.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (123.51 kB)
15.62 ✔ Got BiocVersion 3.18.1 (source) (973 B)
15.63 ✔ Got magrittr 2.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (221.00 kB)
15.87 ✔ Got pillar 1.9.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (646.16 kB)
15.95 ✔ Got BiocIO 1.12.0 (source) (231.34 kB)
16.03 ✔ Got BiocFileCache 2.10.2 (source) (299.52 kB)
16.05 ✔ Got AnnotationFilter 1.26.0 (source) (324.78 kB)
16.13 ✔ Got labeling 0.4.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (60.03 kB)
16.21 ✔ Got utf8 1.2.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (146.77 kB)
16.22 ✔ Got tibble 3.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (672.10 kB)
16.28 ✔ Got AnnotationHub 3.10.1 (source) (994.80 kB)
16.38 ✔ Got isoband 0.2.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.64 MB)
16.60 ✔ Got digest 0.6.34 (x86_64-pc-linux-gnu-ubuntu-22.04) (207.17 kB)
17.03 ✔ Got tweenr 2.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (459.85 kB)
17.13 ✔ Got yulab.utils 0.1.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (76.19 kB)
17.16 ✔ Got cellranger 1.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (100.74 kB)
17.22 ✔ Got ggforce 0.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.83 MB)
17.24 ✔ Got lambda.r 1.2.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (109.83 kB)
17.32 ✔ Got fgsea 1.28.0 (source) (4.95 MB)
17.65 ✔ Got BiocManager 1.30.22 (x86_64-pc-linux-gnu-ubuntu-22.04) (499.02 kB)
17.70 ✔ Got DBI 1.2.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (890.85 kB)
17.84 ✔ Got fontawesome 0.5.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.37 MB)
17.94 ✔ Got png 0.1-8 (x86_64-pc-linux-gnu-ubuntu-22.04) (40.02 kB)
18.01 ✔ Got mime 0.12 (x86_64-pc-linux-gnu-ubuntu-22.04) (33.10 kB)
18.03 ✔ Got commonmark 1.9.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (146.31 kB)
18.08 ✔ Got crosstalk 1.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (406.65 kB)
18.19 ✔ Got lazyeval 0.2.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (155.23 kB)
18.33 ✔ Got interactiveDisplayBase 1.40.0 (source) (7.76 kB)
18.35 ✔ Got restfulr 0.0.15 (source) (15.12 kB)
18.36 ✔ Got sourcetools 0.1.7-1 (x86_64-pc-linux-gnu-ubuntu-22.04) (46.00 kB)
18.53 ✔ Got RCurl 1.98-1.14 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.06 MB)
18.55 ✔ Got sys 3.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (40.17 kB)
18.70 ✔ Got RColorBrewer 1.1-3 (x86_64-pc-linux-gnu-ubuntu-22.04) (53.11 kB)
18.81 ✔ Got statmod 1.5.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (310.78 kB)
18.92 ✔ Got zlibbioc 1.48.2 (source) (382.67 kB)
19.01 ✔ Got dbplyr 2.4.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.20 MB)
19.07 ✔ Got DelayedArray 0.28.0 (source) (624.17 kB)
19.08 ✔ Got tinytex 0.49 (x86_64-pc-linux-gnu-ubuntu-22.04) (137.03 kB)
19.13 ✔ Got promises 1.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.65 MB)
19.23 ✔ Got numDeriv 2016.8-1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (113.11 kB)
19.30 ✔ Got GenomicFeatures 1.54.4 (source) (1.18 MB)
19.45 ✔ Got fdrtool 1.2.17 (x86_64-pc-linux-gnu-ubuntu-22.04) (137.71 kB)
19.47 ✔ Got polynom 1.4-1 (x86_64-pc-linux-gnu-ubuntu-22.04) (404.72 kB)
19.67 ✔ Got genefilter 1.84.0 (source) (993.57 kB)
19.69 ✔ Got plyr 1.8.9 (x86_64-pc-linux-gnu-ubuntu-22.04) (817.98 kB)
19.92 ✔ Got GenomicAlignments 1.38.2 (source) (2.27 MB)
19.93 ✔ Got clipr 0.8.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (50.10 kB)
20.02 ✔ Got RcppArmadillo 0.12.8.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.08 MB)
20.05 ✔ Got ggsci 3.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.43 MB)
20.15 ✔ Got ComplexHeatmap 2.18.0 (source) (1.46 MB)
20.20 ✔ Got treeio 1.26.0 (source) (692.84 kB)
20.29 ✔ Got ensembldb 2.26.0 (source) (3.36 MB)
20.34 ✔ Got downloader 0.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (21.76 kB)
20.36 ✔ Got haven 2.5.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (376.61 kB)
20.60 ✔ Got scatterpie 0.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (133.08 kB)
20.79 ✔ Got ape 5.7-1 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.07 MB)
21.66 ✔ Got tidyr 1.3.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.17 MB)
21.83 ✔ Got gtools 3.9.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (355.84 kB)
21.91 ✔ Got DOSE 3.28.2 (source) (6.81 MB)
21.94 ✔ Got assertthat 0.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (52.32 kB)
22.06 ✔ Got Hmisc 5.1-1 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.52 MB)
22.07 ✔ Got lme4 1.1-35.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.24 MB)
22.15 ✔ Got repr 1.1.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (121.44 kB)
22.21 ✔ Got plotly 4.10.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.20 MB)
22.31 ✔ Got apeglm 1.24.0 (source) (1.11 MB)
22.52 ✔ Got base64url 1.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (24.17 kB)
22.68 ✔ Got MCDA 0.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (620.97 kB)
22.71 ✔ Got RcppNumerical 0.6-0 (x86_64-pc-linux-gnu-ubuntu-22.04) (227.65 kB)
22.75 ✔ Got combinat 0.0-8 (x86_64-pc-linux-gnu-ubuntu-22.04) (40.28 kB)
22.92 ✔ Got FNN 1.1.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (125.99 kB)
23.03 ✔ Got igraph 2.0.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (5.43 MB)
23.18 ✔ Got uwot 0.1.16 (x86_64-pc-linux-gnu-ubuntu-22.04) (682.78 kB)
23.29 ✔ Got fansi 1.0.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (307.86 kB)
23.41 ✔ Got Biostrings 2.70.3 (source) (12.74 MB)
23.49 ✔ Got rlist 0.4.6.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (243.63 kB)
23.64 ✔ Got RcppAnnoy 0.0.22 (x86_64-pc-linux-gnu-ubuntu-22.04) (264.31 kB)
23.85 ✔ Got viridisLite 0.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.30 MB)
23.93 ✔ Got fastmap 1.1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (61.81 kB)
24.00 ✔ Got munsell 0.5.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (243.61 kB)
24.05 ✔ Got hms 1.1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (98.39 kB)
24.17 ✔ Got cowplot 1.1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.38 MB)
24.23 ✔ Got rematch 2.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (15.95 kB)
24.29 ✔ Got farver 2.1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.46 MB)
24.40 ✔ Got colorspace 2.1-0 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.59 MB)
24.54 ✔ Got fs 1.6.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (288.29 kB)
24.64 ✔ Got blob 1.2.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (45.94 kB)
24.75 ✔ Got later 1.3.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (130.82 kB)
24.81 ✔ Got formatR 1.14 (x86_64-pc-linux-gnu-ubuntu-22.04) (150.68 kB)
24.90 ✔ Got ellipsis 0.3.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (33.57 kB)
24.94 ✔ Got dplyr 1.1.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.47 MB)
25.04 ✔ Got ProtGenerics 1.34.0 (source) (8.89 kB)
25.05 ✔ Got RCy3 2.22.1 (source) (6.77 MB)
25.07 ✔ Got highr 0.10 (x86_64-pc-linux-gnu-ubuntu-22.04) (38.96 kB)
25.15 ✔ Got KEGGREST 1.42.0 (source) (22.41 kB)
25.42 ✔ Got xtable 1.8-4 (x86_64-pc-linux-gnu-ubuntu-22.04) (700.94 kB)
25.50 ✔ Got DT 0.32 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.79 MB)
25.83 ✔ Got locfit 1.5-9.8 (x86_64-pc-linux-gnu-ubuntu-22.04) (531.61 kB)
26.05 ✔ Got ggsignif 0.6.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (601.84 kB)
26.11 ✔ Got GOSemSim 2.28.1 (source) (608.12 kB)
26.26 ✔ Got car 3.1-2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.71 MB)
26.34 ✔ Got enrichplot 1.22.0 (source) (108.62 kB)
26.57 ✔ Got sass 0.4.8 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.41 MB)
26.59 ✔ Got limma 3.58.1 (source) (2.80 MB)
26.60 ✔ Got aplot 0.2.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (63.68 kB)
26.69 ✔ Got Rsamtools 2.18.0 (source) (2.92 MB)
26.78 ✔ Got ggtree 3.10.1 (source) (362.60 kB)
27.08 ✔ Got vroom 1.6.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (926.34 kB)
27.09 ✔ Got rtracklayer 1.62.0 (source) (4.02 MB)
27.11 ✔ Got shiny 1.8.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.45 MB)
27.20 ✔ Got rmarkdown 2.25 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.61 MB)
27.29 ✔ Got Rhtslib 2.4.1 (source) (4.58 MB)
27.31 ✔ Got GetoptLong 1.0.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.07 MB)
27.34 ✔ Got flashClust 1.01-2 (x86_64-pc-linux-gnu-ubuntu-22.04) (20.41 kB)
27.41 ✔ Got futile.logger 1.4.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (94.16 kB)
27.54 ✔ Got checkmate 2.3.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (716.97 kB)
27.91 ✔ Got graphlayouts 1.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.78 MB)
28.11 ✔ Got openxlsx 4.2.5.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.02 MB)
28.21 ✔ Got ggbeeswarm 0.7.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.75 MB)
28.22 ✔ Got coda 0.19-4.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (322.31 kB)
28.26 ✔ Got emdbook 1.3.13 (x86_64-pc-linux-gnu-ubuntu-22.04) (204.18 kB)
28.53 ✔ Got pROC 1.18.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (829.92 kB)
28.59 ✔ Got glpkAPI 1.3.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.13 MB)
28.75 ✔ Got networkD3 0.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (188.44 kB)
28.81 ✔ Got generics 0.1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (76.08 kB)
28.92 ✔ Got emmeans 1.10.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.15 MB)
29.02 ✔ Got stringr 1.5.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (305.30 kB)
29.05 ✔ Got gtable 0.3.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (215.93 kB)
29.12 ✔ Got tidyselect 1.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (219.93 kB)
29.25 ✔ Got RcppEigen 0.3.3.9.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.53 MB)
29.32 ✔ Got base64enc 0.1-3 (x86_64-pc-linux-gnu-ubuntu-22.04) (26.09 kB)
29.43 ✔ Got bit64 4.0.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (475.47 kB)
29.58 ✔ Got gridGraphics 0.5-1 (x86_64-pc-linux-gnu-ubuntu-22.04) (248.73 kB)
29.65 ✔ Got askpass 1.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (21.51 kB)
29.71 ✔ Got polyclip 1.10-6 (x86_64-pc-linux-gnu-ubuntu-22.04) (117.73 kB)
29.85 ✔ Got purrr 1.0.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (488.94 kB)
29.88 ✔ Got lpsymphony 1.30.0 (source) (12.42 MB)
29.95 ✔ Got futile.options 1.0.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (18.12 kB)
30.01 ✔ Got systemfonts 1.0.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (243.37 kB)
30.07 ✔ Got httpuv 1.6.14 (x86_64-pc-linux-gnu-ubuntu-22.04) (598.62 kB)
30.18 ✔ Got rjson 0.2.21 (x86_64-pc-linux-gnu-ubuntu-22.04) (150.49 kB)
30.23 ✔ Got prettyunits 1.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (155.03 kB)
30.27 ✔ Got XVector 0.42.0 (source) (67.83 kB)
30.36 ✔ Got S4Arrays 1.2.1 (source) (282.09 kB)
30.58 ✔ Got SparseArray 1.2.4 (source) (367.78 kB)
30.67 ✔ Got rstatix 0.7.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (605.34 kB)
30.74 ✔ Got IRanges 2.36.0 (source) (481.06 kB)
30.77 ✔ Got foreach 1.5.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (138.01 kB)
30.91 ✔ Got openssl 2.1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.31 MB)
31.07 ✔ Got affy 1.80.0 (source) (1.22 MB)
31.10 ✔ Got GlobalOptions 0.1.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (469.68 kB)
31.18 ✔ Got knitr 1.45 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.47 MB)
31.19 ✔ Got htmlwidgets 1.6.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (813.47 kB)
31.29 ✔ Got tximeta 1.20.3 (source) (1.68 MB)
31.31 ✔ Got clusterProfiler 4.10.1 (source) (624.15 kB)
31.42 ✔ Got forcats 1.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (421.90 kB)
31.43 ✔ Got Biobase 2.62.0 (source) (1.80 MB)
31.45 ✔ Got biomaRt 2.58.2 (source) (670.06 kB)
31.53 ✔ Got ggnewscale 0.4.10 (x86_64-pc-linux-gnu-ubuntu-22.04) (344.20 kB)
31.63 ✔ Got tzdb 0.4.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (640.81 kB)
31.65 ✔ Got caTools 1.18.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (199.81 kB)
31.73 ✔ Got mgcv 1.9-1 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.25 MB)
31.81 ✔ Got shape 1.4.6.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (745.72 kB)
31.95 ✔ Got rstudioapi 0.15.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (292.72 kB)
32.08 ✔ Got bdsmatrix 1.3-6 (x86_64-pc-linux-gnu-ubuntu-22.04) (299.76 kB)
32.18 ✔ Got ellipse 0.5.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (216.90 kB)
32.29 ✔ Got multcompView 0.1-9 (x86_64-pc-linux-gnu-ubuntu-22.04) (114.56 kB)
32.43 ✔ Got bslib 0.6.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (6.21 MB)
32.46 ✔ Got bbmle 1.0.25.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (884.80 kB)
32.50 ✔ Got triangle 1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (105.23 kB)
32.77 ✔ Got egg 0.4.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (825.41 kB)
32.82 ✔ Got memoise 2.0.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (47.79 kB)
32.87 ✔ Got pbmcapply 1.5.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (39.75 kB)
32.89 ✔ Got factoextra 1.0.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (414.44 kB)
32.98 ✔ Got progress 1.2.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (84.60 kB)
33.03 ✔ Got bitops 1.0-7 (x86_64-pc-linux-gnu-ubuntu-22.04) (24.85 kB)
33.31 ✔ Got RJSONIO 1.3-1.9 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.04 MB)
33.48 ✔ Got crayon 1.5.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (159.79 kB)
33.72 ✔ Got jquerylib 0.1.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (526.60 kB)
33.78 ✔ Got affyio 1.72.0 (source) (110.38 kB)
33.85 ✔ Got ggfortify 0.4.16 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.20 MB)
33.92 ✔ Got yaml 2.3.8 (x86_64-pc-linux-gnu-ubuntu-22.04) (114.14 kB)
33.94 ✔ Got snow 0.4-4 (x86_64-pc-linux-gnu-ubuntu-22.04) (95.64 kB)
33.96 ✔ Got tximport 1.30.0 (source) (315.63 kB)
34.04 ✔ Got sva 3.50.0 (source) (452.89 kB)
34.09 ✔ Got BiocGenerics 0.48.1 (source) (49.55 kB)
34.19 ✔ Got BiocParallel 1.36.0 (source) (997.12 kB)
34.33 ✔ Got rhdf5 2.46.1 (source) (1.27 MB)
34.34 ✔ Got slam 0.1-50 (x86_64-pc-linux-gnu-ubuntu-22.04) (184.46 kB)
34.47 ✔ Got dendextend 1.17.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.90 MB)
34.48 ✔ Got minqa 1.2.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (118.15 kB)
34.76 ✔ Got ggpubr 0.6.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.09 MB)
34.93 ✔ Got qvalue 2.34.0 (source) (2.77 MB)
35.06 ✔ Got nloptr 2.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (710.25 kB)
35.07 ✔ Got GenomeInfoDbData 1.2.11 (source) (12.28 MB)
35.28 ✔ Got Formula 1.2-5 (x86_64-pc-linux-gnu-ubuntu-22.04) (158.37 kB)
35.33 ✔ Got gson 0.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (231.88 kB)
35.35 ✔ Got shadowtext 0.1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (216.34 kB)
35.40 ✔ Got IRdisplay 1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (31.34 kB)
35.43 ✔ Got uuid 1.2-0 (x86_64-pc-linux-gnu-ubuntu-22.04) (47.70 kB)
35.64 ✔ Got mvtnorm 1.2-4 (x86_64-pc-linux-gnu-ubuntu-22.04) (744.87 kB)
36.07 ✔ Got tidygraph 1.3.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (553.00 kB)
36.09 ✔ Got leidenbase 0.1.27 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.32 MB)
36.19 ✔ Got gridExtra 2.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.11 MB)
36.28 ✔ Got ggplotify 0.1.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (139.89 kB)
36.56 ✔ Got rlang 1.1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.55 MB)
36.67 ✔ Got fastmatch 1.1-4 (x86_64-pc-linux-gnu-ubuntu-22.04) (34.50 kB)
36.69 ✔ Got preprocessCore 1.64.0 (source) (124.00 kB)
36.79 ✔ Got rappdirs 0.3.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (43.88 kB)
36.92 ✔ Got bit 4.0.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.13 MB)
37.14 ✔ Got MatrixModels 0.5-3 (x86_64-pc-linux-gnu-ubuntu-22.04) (413.22 kB)
37.26 ✔ Got FactoMineR 2.9 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.79 MB)
37.30 ✔ Got xfun 0.42 (x86_64-pc-linux-gnu-ubuntu-22.04) (466.84 kB)
37.36 ✔ Got pbkrtest 0.5.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (186.59 kB)
37.37 ✔ Got reshape2 1.4.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (37.82 kB)
37.40 ✔ Got backports 1.4.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (95.02 kB)
37.42 ✔ Got rhdf5filters 1.14.1 (source) (1.18 MB)
37.54 ✔ Got graph 1.80.0 (source) (1.50 MB)
37.63 ✔ Got vsn 3.70.0 (source) (1.84 MB)
37.98 ✔ Got corrplot 0.92 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.84 MB)
38.00 ✔ Got ggfun 0.1.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (196.78 kB)
38.05 ✔ Got leaps 3.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (80.49 kB)
38.07 ✔ Got DESeq2 1.42.1 (source) (2.10 MB)
38.16 ✔ Got doParallel 1.0.17 (x86_64-pc-linux-gnu-ubuntu-22.04) (187.66 kB)
38.28 ✔ Got leidenAlg 1.1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (252.14 kB)
38.38 ✔ Got abind 1.4-5 (x86_64-pc-linux-gnu-ubuntu-22.04) (61.33 kB)
38.43 ✔ Got edgeR 4.0.16 (source) (3.57 MB)
38.62 ✔ Got pbdZMQ 0.3-11 (x86_64-pc-linux-gnu-ubuntu-22.04) (546.45 kB)
39.07 ✔ Got GSEABase 1.64.0 (source) (299.04 kB)
39.20 ✔ Got BH 1.84.0-0 (x86_64-pc-linux-gnu-ubuntu-22.04) (13.03 MB)
39.33 ✔ Got ggraph 2.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.50 MB)
39.61 ✔ Got S4Vectors 0.40.2 (source) (838.19 kB)
39.72 ✔ Got viridis 0.6.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.01 MB)
39.74 ✔ Got annotate 1.80.0 (source) (1.50 MB)
39.85 ✔ Got ggplot2 3.5.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.81 MB)
39.95 ✔ Got htmlTable 2.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (410.32 kB)
40.04 ✔ Got XML 3.99-0.16.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.81 MB)
40.07 ✔ Got data.table 1.15.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.18 MB)
40.19 ✔ Got ggrepel 0.9.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (281.80 kB)
40.33 ✔ Got withr 3.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (237.91 kB)
40.41 ✔ Got pkgconfig 2.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (17.58 kB)
40.50 ✔ Got clue 0.3-65 (x86_64-pc-linux-gnu-ubuntu-22.04) (991.62 kB)
40.52 ✔ Got VennDiagram 1.7.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (248.11 kB)
40.66 ✔ Got circlize 0.4.16 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.31 MB)
40.83 ✔ Got AnnotationDbi 1.64.1 (source) (4.36 MB)
40.92 ✔ Got cachem 1.0.8 (x86_64-pc-linux-gnu-ubuntu-22.04) (66.19 kB)
40.98 ✔ Got evaluate 0.23 (x86_64-pc-linux-gnu-ubuntu-22.04) (81.84 kB)
41.06 ✔ Got iterators 1.0.14 (x86_64-pc-linux-gnu-ubuntu-22.04) (345.45 kB)
41.27 ✔ Got scales 1.3.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (698.10 kB)
41.52 ✔ Got patchwork 1.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.29 MB)
41.57 ✔ Got estimability 1.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (48.27 kB)
41.72 ✔ Got cpp11 0.4.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (280.14 kB)
41.86 ✔ Got stringi 1.8.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.27 MB)
41.95 ✔ Got SparseM 1.81 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.04 MB)
42.14 ✔ Got IHW 1.30.0 (source) (3.75 MB)
42.29 ✔ Got IRkernel 1.3.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (227.64 kB)
42.44 ✔ Got pheatmap 1.0.12 (x86_64-pc-linux-gnu-ubuntu-22.04) (76.69 kB)
42.50 ✔ Got irlba 2.3.5.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (291.74 kB)
42.61 ✔ Got SummarizedExperiment 1.32.0 (source) (686.05 kB)
42.85 ✔ Got quantreg 5.97 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.55 MB)
42.88 ✔ Got xml2 1.3.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (274.69 kB)
42.89 ✔ Got readxl 1.4.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (862.07 kB)
42.99 ✔ Got Rglpk 0.6-5.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (58.30 kB)
43.02 ✔ Got matrixStats 1.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (465.65 kB)
43.07 ✔ Got MatrixGenerics 1.14.0 (source) (31.23 kB)
43.08 ✔ Got GSA 1.03.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (99.60 kB)
43.24 ✔ Got Rhdf5lib 1.24.2 (source) (12.06 MB)
43.33 ✔ Got sccore 1.0.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (870.59 kB)
43.44 ✔ Got htmltools 0.5.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (349.66 kB)
43.48 ✔ Got gplots 3.1.3.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (595.03 kB)
43.65 ✔ Got tidytree 0.4.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (340.65 kB)
43.78 ✔ Got broom 1.0.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.85 MB)
43.97 ✔ Got scatterplot3d 0.3-44 (x86_64-pc-linux-gnu-ubuntu-22.04) (348.01 kB)
44.01 ✔ Got vctrs 0.6.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.29 MB)
44.21 ✔ Got HDO.db 0.99.1 (source) (1.86 MB)
44.47 ✔ Got beeswarm 0.4.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (77.21 kB)
44.63 ✔ Got GenomicRanges 1.54.1 (source) (1.14 MB)
44.67 ✔ Got carData 3.0-5 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.82 MB)
44.68 ✔ Got vipor 0.4.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.58 MB)
44.74 ✔ Got Cairo 1.6-2 (x86_64-pc-linux-gnu-ubuntu-22.04) (82.59 kB)
44.88 ✔ Got httr 1.4.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (468.06 kB)
45.06 ✔ Got readr 2.1.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (825.95 kB)
45.34 ✔ Got GenomeInfoDb 1.38.8 (source) (3.58 MB)
45.54 ✔ Got RSQLite 2.3.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.31 MB)
45.60 ✔ Got Rcpp 1.0.12 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.15 MB)
45.90 ✔ Got hexbin 1.28.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.60 MB)
47.91 ✔ Got GO.db 3.18.0 (source) (29.01 MB)
47.95 ✔ Got nlme 3.1-164 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.32 MB)
48.50 ✔ Got hcocena 1.1.1 (source) (61.65 MB)
54.27 ✔ Got org.Hs.eg.db 3.18.0 (source) (97.92 MB)
59.11 ✔ Got org.Mm.eg.db 3.18.0 (source) (80.89 MB)
59.13 ℹ Installing system requirements
59.13 ℹ Executing `sh -c apt-get -y update`
63.86 ℹ Executing `sh -c apt-get -y install libicu-dev libfontconfig1-dev libfreetype6-dev zlib1g-dev pandoc libpng-dev libxml2-dev cmake libglpk-dev libzmq3-dev libcairo2-dev`
89.32 ℹ Building BiocVersion 3.18.1
89.48 ℹ Building ProtGenerics 1.34.0
89.51 ℹ Building zlibbioc 1.48.2
89.62 ℹ Building GenomeInfoDbData 1.2.11
89.88 ℹ Building preprocessCore 1.64.0
89.97 ℹ Building tximport 1.30.0
90.09 ℹ Building Rhdf5lib 1.24.2
90.34 ℹ Building lpsymphony 1.30.0
91.68 ℹ Building BiocGenerics 0.48.1
92.12 ✔ Built BiocVersion 3.18.1 (2.6s)
92.15 ✔ Built ProtGenerics 1.34.0 (2.6s)
92.16 ✔ Built zlibbioc 1.48.2 (2.5s)
92.18 ✔ Built GenomeInfoDbData 1.2.11 (2.3s)
92.21 ✔ Built tximport 1.30.0 (2.1s)
92.25 ✔ Installed glue 1.7.0  (439ms)
92.27 ✔ Installed lifecycle 1.0.4  (449ms)
92.30 ✔ Installed magrittr 2.0.3  (455ms)
92.33 ✔ Installed rlang 1.1.3  (471ms)
92.35 ✔ Installed stringi 1.8.3  (488ms)
92.40 ✔ Installed stringr 1.5.1  (529ms)
92.43 ✔ Installed vctrs 0.6.5  (544ms)
92.45 ✔ Installed gridExtra 2.3  (555ms)
92.47 ✔ Installed gtable 0.3.4  (569ms)
92.49 ✔ Installed GSA 1.03.2  (580ms)
92.51 ✔ Installed colorspace 2.1-0  (569ms)
92.54 ✔ Installed cpp11 0.4.7  (578ms)
92.56 ✔ Installed fansi 1.0.6  (587ms)
92.58 ✔ Installed farver 2.1.1  (596ms)
92.63 ✔ Installed ggforce 0.4.2  (610ms)
92.67 ✔ Installed isoband 0.2.7  (659ms)
92.69 ✔ Installed labeling 0.4.3  (674ms)
92.71 ✔ Installed munsell 0.5.0  (687ms)
92.74 ✔ Installed pillar 1.9.0  (701ms)
92.76 ✔ Installed pkgconfig 2.0.3  (714ms)
92.79 ✔ Installed polyclip 1.10-6  (727ms)
92.82 ✔ Installed Rcpp 1.0.12  (753ms)
92.85 ✔ Installed RcppEigen 0.3.3.9.4  (771ms)
92.92 ✔ Installed systemfonts 1.0.5  (80ms)
92.97 ✔ Installed tibble 3.2.1  (93ms)
93.00 ✔ Installed tidyselect 1.2.0  (59ms)
93.04 ✔ Installed tweenr 2.0.3  (54ms)
93.08 ✔ Installed utf8 1.2.4  (54ms)
93.12 ✔ Installed viridisLite 0.4.2  (54ms)
93.16 ✔ Installed withr 3.0.0  (56ms)
93.20 ✔ Installed generics 0.1.3  (56ms)
93.24 ✔ Installed ggfortify 0.4.16  (54ms)
93.32 ✔ Installed purrr 1.0.2  (90ms)
93.35 ✔ Installed cachem 1.0.8  (58ms)
93.39 ✔ Installed digest 0.6.34  (52ms)
93.43 ✔ Installed fastmap 1.1.1  (52ms)
93.47 ✔ Installed fs 1.6.3  (54ms)
93.51 ✔ Installed ggplotify 0.1.2  (57ms)
93.55 ✔ Installed gridGraphics 0.5-1  (53ms)
93.58 ✔ Installed memoise 2.0.1  (52ms)
93.66 ✔ Installed yulab.utils 0.1.4  (78ms)
93.70 ✔ Installed cowplot 1.1.3  (89ms)
93.73 ✔ Installed corrplot 0.92  (51ms)
93.82 ✔ Installed fastmatch 1.1-4  (34ms)
93.87 ✔ Installed data.table 1.15.0  (105ms)
93.90 ✔ Installed formatR 1.14  (54ms)
93.94 ✔ Installed futile.options 1.0.1  (48ms)
93.98 ✔ Installed lambda.r 1.2.4  (48ms)
94.05 ✔ Installed snow 0.4-4  (72ms)
94.13 ✔ Installed dplyr 1.1.4  (118ms)
94.17 ✔ Installed cellranger 1.1.0  (59ms)
94.21 ✔ Installed crayon 1.5.2  (51ms)
94.25 ✔ Installed hms 1.1.3  (51ms)
94.29 ✔ Installed prettyunits 1.2.0  (53ms)
94.31 ✔ Built BiocGenerics 0.48.1 (2.5s)
94.35 ✔ Installed progress 1.2.3  (74ms)
94.39 ✔ Installed readxl 1.4.3  (78ms)
94.45 ✔ Installed rematch 2.0.0  (53ms)
94.50 ✔ Installed BH 1.84.0-0  (775ms)
94.52 ✔ Installed abind 1.4-5  (110ms)
94.56 ✔ Installed askpass 1.2.0  (78ms)
94.59 ✔ Installed base64enc 0.1-3  (51ms)
94.63 ✔ Installed BiocManager 1.30.22  (53ms)
94.67 ✔ Installed bit 4.0.5  (54ms)
94.71 ✔ Installed bit64 4.0.5  (55ms)
94.74 ✔ Installed bitops 1.0-7  (49ms)
94.81 ✔ Installed blob 1.2.4  (73ms)
94.85 ✔ Installed bslib 0.6.1  (82ms)
94.88 ✔ Installed commonmark 1.9.1  (49ms)
94.92 ✔ Installed crosstalk 1.2.1  (49ms)
94.96 ✔ Installed DBI 1.2.2  (54ms)
95.04 ✔ Installed dbplyr 2.4.0  (77ms)
95.08 ✔ Installed ellipsis 0.3.2  (15ms)
95.11 ✔ Installed DT 0.32  (123ms)
95.18 ✔ Installed evaluate 0.23  (49ms)
95.22 ✔ Installed fontawesome 0.5.2  (82ms)
95.25 ✔ Installed highr 0.10  (51ms)
95.29 ✔ Installed htmltools 0.5.7  (52ms)
95.33 ✔ Installed htmlwidgets 1.6.4  (52ms)
95.36 ✔ Installed httpuv 1.6.14  (54ms)
95.43 ✔ Installed httr 1.4.7  (65ms)
95.48 ✔ Installed jquerylib 0.1.4  (88ms)
95.52 ✔ Installed knitr 1.45  (57ms)
95.61 ✔ Installed later 1.3.2  (101ms)
95.66 ✔ Installed lazyeval 0.2.2  (81ms)
95.69 ✔ Installed mime 0.12  (50ms)
95.74 ✔ Installed openssl 2.1.1  (53ms)
95.77 ✔ Installed png 0.1-8  (53ms)
95.81 ✔ Installed promises 1.2.1  (51ms)
95.85 ✔ Installed rappdirs 0.3.3  (52ms)
95.88 ✔ Installed RCurl 1.98-1.14  (52ms)
95.94 ✔ Built preprocessCore 1.64.0 (5.9s)
95.97 ✔ Installed rjson 0.2.21  (104ms)
96.01 ✔ Installed rmarkdown 2.25  (103ms)
96.05 ✔ Installed RSQLite 2.3.5  (58ms)
96.09 ✔ Installed sass 0.4.8  (56ms)
96.13 ✔ Installed sourcetools 0.1.7-1  (22ms)
96.17 ✔ Installed shiny 1.8.0  (100ms)
96.20 ✔ Installed sys 3.4.2  (84ms)
96.24 ✔ Installed tinytex 0.49  (85ms)
96.31 ✔ Installed xfun 0.42  (81ms)
96.35 ✔ Installed xml2 1.3.6  (58ms)
96.38 ✔ Installed xtable 1.8-4  (53ms)
96.42 ✔ Installed yaml 2.3.8  (48ms)
96.45 ✔ Installed BiocVersion 3.18.1  (47ms)
96.49 ✔ Installed ProtGenerics 1.34.0  (47ms)
96.53 ✔ Installed zlibbioc 1.48.2  (50ms)
96.53 ℹ Building Rhtslib 2.4.1
96.91 ✔ Installed GenomeInfoDbData 1.2.11  (392ms)
96.93 ℹ Building affyio 1.72.0
97.05 ✔ Installed statmod 1.5.0  (34ms)
97.10 ℹ Building limma 3.58.1
97.27 ✔ Installed preprocessCore 1.64.0  (243ms)
97.34 ✔ Installed tximport 1.30.0  (44ms)
97.42 ✔ Installed locfit 1.5-9.8  (66ms)
97.46 ✔ Installed mgcv 1.9-1  (95ms)
97.50 ✔ Installed nlme 3.1-164  (59ms)
97.54 ✔ Installed RColorBrewer 1.1-3  (55ms)
97.58 ✔ Installed pheatmap 1.0.12  (55ms)
97.62 ✔ Installed fdrtool 1.2.17  (54ms)
97.66 ✔ Installed slam 0.1-50  (55ms)
97.70 ✔ Installed XML 3.99-0.16.1  (58ms)
97.81 ✔ Installed backports 1.4.1  (56ms)
97.89 ✔ Installed broom 1.0.5  (166ms)
97.94 ✔ Installed car 3.1-2  (105ms)
98.01 ✔ Installed carData 3.0-5  (84ms)
98.05 ✔ Installed ggpubr 0.6.0  (81ms)
98.09 ✔ Installed ggsci 3.0.0  (60ms)
98.14 ✔ Installed ggsignif 0.6.4  (57ms)
98.18 ✔ Installed lme4 1.1-35.1  (58ms)
98.25 ✔ Installed MatrixModels 0.5-3  (55ms)
98.29 ✔ Installed minqa 1.2.6  (93ms)
98.33 ✔ Installed nloptr 2.0.3  (55ms)
98.37 ✔ Installed numDeriv 2016.8-1.1  (52ms)
98.41 ✔ Installed pbkrtest 0.5.2  (52ms)
98.44 ✔ Installed polynom 1.4-1  (52ms)
98.48 ✔ Installed quantreg 5.97  (51ms)
98.52 ✔ Installed rstatix 0.7.2  (56ms)
98.56 ✔ Installed SparseM 1.81  (52ms)
98.64 ✔ Installed plyr 1.8.9  (93ms)
102.5 Error: 
102.5 ! error in pak subprocess
102.5 Caused by error in `verify_extracted_package(filename, pkg_cache)`:
102.5 ! 
102.5 '/tmp/Rtmp6FU1kx/file3415e097bd/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.3/reshape2_1.4.4.tar.gz'
102.5 is not a valid binary, it is missing reshape2/Meta/package.rds.
102.5 ---
102.5 Backtrace:
102.5 1. pak::pak(packages)
102.5 2. pak::pkg_install(pkg, ...)
102.5 3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
102.5 4. err$throw(res$error)
102.5 ---
102.5 Subprocess backtrace:
102.5  1. base::withCallingHandlers(cli_message = function(msg) { …
102.5  2. get("pkg_install_do_plan", asNamespace("pak"))(...)
102.5  3. proposal$install()
102.5  4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
102.5  5. base::withCallingHandlers({ …
102.5  6. pkgdepends:::handle_events(state, events)
102.5  7. pkgdepends:::handle_event(state, i)
102.5  8. proc$get_result()
102.5  9. processx:::process_get_result(self, private)
102.5 10. private$post_process()
102.5 11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
102.5 12. pkgdepends:::verify_extracted_package(filename, pkg_cache)
102.5 13. base::throw(pkg_error("{.path {filename}} is not a valid binary, it is missing {…
102.5 14. | base::signalCondition(cond)
102.5 15. global (function (e) …
102.5 Execution halted
------
Dockerfile:23
--------------------
  21 |     COPY stage_1_packages.txt /tmp/
  22 |     
  23 | >>> RUN R -e "packages <- readLines('/tmp/stage_1_packages.txt'); pak::pak(packages); pak::cache_clean()"
  24 |     
  25 |     RUN rm /tmp/stage_*_packages.txt
--------------------
ERROR: failed to solve: process "/bin/sh -c R -e \"packages <- readLines('/tmp/stage_1_packages.txt'); pak::pak(packages); pak::cache_clean()\"" did not complete successfully: exit code: 1

@danielloader
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Can confirm also hitting this issue, can't build a docker image that used to build fine any more (last built it late 2023 but maybe 20-30 times in a month back then with no failures) - now I'm struggling to get any builds in Github Actions to succeed at all.

@gaborcsardi
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Member

I can't reproduce this, for me PPPM sends:

✔ Got reshape2 1.4.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (115.01 kB)

whereas in your output you get

37.37 ✔ Got reshape2 1.4.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (37.82 kB)

which is clearly a different package file. So for you PPPM sends a source package instead of a binary package.

This should not matter here, but it is easier and much faster to install pak from our repo, see https://pak.r-lib.org/reference/install.html#pre-built-binaries
and you definitely don't need to install pkgdepends.

@danielloader Which platform? Which PPM repo? Which R package and what version?

@danielloader
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danielloader commented Aug 1, 2024 •
edited
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Dockerfile installs PAK as suggested:

RUN R -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'

R 4.2, CRAN or https://cloud.r-project.org, Reshape2 1.4.4.

0.406                                                                                                                                                                                                                                                                                                                                                                                           
0.406 R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"                                                                                                                                                                                                                                                                                                                                        
0.406 Copyright (C) 2023 The R Foundation for Statistical Computing                                                                                                                                                                                                                                                                                                                             
0.406 Platform: x86_64-pc-linux-gnu (64-bit)                                                                                                                                                                                                                                                                                                                                                    
0.406 
0.406 R is free software and comes with ABSOLUTELY NO WARRANTY.
0.406 You are welcome to redistribute it under certain conditions.
0.406 Type 'license()' or 'licence()' for distribution details.
0.406 
0.406 R is a collaborative project with many contributors.
0.406 Type 'contributors()' for more information and
0.406 'citation()' on how to cite R or R packages in publications.
0.406 
0.406 Type 'demo()' for some demos, 'help()' for on-line help, or
0.406 'help.start()' for an HTML browser interface to help.
0.406 Type 'q()' to quit R.
0.406 
0.571 > pak::pak()
1.774 ! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
1.847 
3.249 v Updated metadata database: 3.48 MB in 9 files.
3.250 
3.256 i Updating metadata database
6.521 v Updating metadata database ... done
6.522 
7.511  
7.516 > Will install 119 packages.
7.527 > Will update 3 packages.
7.533 > Will download 123 packages with unknown size.
7.541 + DT                        0.27     [dl]
7.541 + MASS           7.3-58.2 > 7.3-58.3 [dl]
7.541 + Matrix         1.5-3    > 1.5-4    [dl]
7.541 + R.cache                   0.16.0   [dl]
7.541 + R.methodsS3               1.8.2    [dl]
7.541 + R.oo                      1.25.0   [dl]
7.541 + R.utils                   2.12.2   [dl]
7.541 + R6                        2.5.1    [dl]
7.541 + RColorBrewer              1.1-3    [dl]
7.541 + Rcpp                      1.0.10   [dl]
7.541 + actuar                    3.3-2    [dl]
7.541 + anytime                   0.3.9    [dl]
7.541 + askpass                   1.1      [dl]
7.541 + attempt                   0.3.1    [dl]
7.541 + backports                 1.4.1    [dl]
7.541 + base64enc                 0.1-3    [dl]
7.541 + brew                      1.0-8    [dl]
7.541 + bslib                     0.4.2    [dl]
7.541 + cachem                    1.0.7    [dl]
7.541 + callr                     3.7.3    [dl]
7.541 + cli                       3.6.1    [dl]
7.541 + collections               0.3.7    [dl]
7.541 + colorspace                2.1-0    [dl]
7.541 + commonmark                1.9.0    [dl]
7.541 + config                    0.3.1    [dl]
7.541 + crayon                    1.5.2    [dl]
7.541 + crosstalk                 1.2.0    [dl]
7.541 + crul                      1.3      [dl]
7.541 + curl                      5.0.0    [dl] + x libcurl4-openssl-dev, x libssl-dev
7.541 + cyclocomp                 1.1.0    [dl]
7.541 + desc                      1.4.2    [dl]
7.541 + digest                    0.6.31   [dl]
7.541 + dplyr                     1.1.1    [dl]
7.541 + dygraphs                  1.1.1.6  [dl]
7.541 + ellipsis                  0.3.2    [dl]
7.541 + evaluate                  0.20     [dl]
7.541 + expint                    0.1-8    [dl]
7.541 + fansi                     1.0.4    [dl]
7.541 + farver                    2.1.1    [dl]
7.541 + fastmap                   1.1.1    [dl]
7.541 + fontawesome               0.5.1    [dl]
7.541 + forcats                   1.0.0    [dl]
7.541 + fs                        1.6.1    [dl] + v make
7.541 + generics                  0.1.3    [dl]
7.541 + ggplot2                   3.4.2    [dl]
7.541 + ggradar                   0.2      [bld][cmp][dl] (GitHub: 53404a5)
7.541 + ghql                      0.1.0    [dl]
7.541 + glue                      1.6.2    [dl]
7.541 + golem                     0.4.0    [dl]
7.541 + graphql                   1.5.1    [dl]
7.541 + gtable                    0.3.3    [dl]
7.541 + here                      1.0.1    [dl]
7.541 + highr                     0.10     [dl]
7.541 + htmltools                 0.5.5    [dl]
7.541 + htmlwidgets               1.6.2    [dl]
7.541 + httpcode                  0.3.0    [dl]
7.541 + httpuv                    1.6.9    [dl] + v make, x zlib1g-dev
7.541 + httr                      1.4.5    [dl]
7.541 + isoband                   0.2.7    [dl]
7.541 + jquerylib                 0.1.4    [dl]
7.541 + jsonlite                  1.8.4    [dl]
7.541 + knitr                     1.42     [dl] + x pandoc
7.541 + labeling                  0.4.2    [dl]
7.541 + languageserver            0.3.15   [dl]
7.541 + later                     1.3.0    [dl]
7.541 + lattice        0.20-45  > 0.21-8   [dl]
7.541 + lazyeval                  0.2.2    [dl]
7.541 + lifecycle                 1.0.3    [dl]
7.541 + lintr                     3.0.2    [dl]
7.541 + logger                    0.2.2    [dl]
7.541 + lubridate                 1.9.2    [dl]
7.541 + magrittr                  2.0.3    [dl]
7.541 + memoise                   2.0.1    [dl]
7.541 + mime                      0.12     [dl]
7.541 + mongolite                 2.7.2    [dl] + x libssl-dev, x libsasl2-dev
7.541 + munsell                   0.5.0    [dl]
7.541 + openssl                   2.0.6    [dl] + x libssl-dev
7.541 + pillar                    1.9.0    [dl]
7.541 + pkgconfig                 2.0.3    [dl]
7.541 + pkgload                   1.3.2    [dl]
7.541 + plyr                      1.8.8    [dl]
7.541 + processx                  3.8.1    [dl]
7.541 + promises                  1.2.0.1  [dl]
7.541 + ps                        1.7.5    [dl]
7.541 + purrr                     1.0.1    [dl]
7.541 + rappdirs                  0.3.3    [dl]
7.541 + remotes                   2.4.2    [dl] + x git
7.541 + reshape2                  1.4.4    [dl]
7.541 + rex                       1.2.1    [dl]
7.541 + rlang                     1.1.0    [dl]
7.541 + rlog                      0.1.0    [dl]
7.541 + rmarkdown                 2.21     [dl] + x pandoc
7.541 + roxygen2                  7.2.3    [dl]
7.541 + rprojroot                 2.0.3    [dl]
7.541 + sass                      0.4.5    [dl] + v make
7.541 + scales                    1.2.1    [dl]
7.541 + shiny                     1.7.4    [dl]
7.541 + shinyWidgets              0.7.6    [dl]
7.541 + shinydashboard            0.7.2    [dl]
7.541 + sourcetools               0.1.7-1  [dl]
7.541 + stringi                   1.7.12   [dl] + x libicu-dev
7.541 + stringr                   1.5.0    [dl]
7.541 + styler                    1.9.1    [dl]
7.541 + sys                       3.4.1    [dl]
7.541 + tibble                    3.2.1    [dl]
7.541 + tidyr                     1.3.0    [dl]
7.541 + tidyselect                1.2.0    [dl]
7.541 + timechange                0.2.0    [dl]
7.541 + tinytex                   0.45     [dl]
7.541 + triebeard                 0.4.1    [dl]
7.541 + urltools                  1.7.3    [dl]
7.541 + utf8                      1.2.3    [dl]
7.541 + vctrs                     0.6.2    [dl]
7.541 + viridisLite               0.4.1    [dl]
7.541 + withr                     2.5.0    [dl]
7.541 + xfun                      0.38     [dl]
7.541 + xml2                      1.3.3    [dl] + x libxml2-dev
7.541 + xmlparsedata              1.0.5    [dl]
7.541 + xtable                    1.8-4    [dl]
7.541 + xts                       0.13.1   [dl]
7.541 + yaml                      2.3.7    [dl]
7.541 + zoo                       1.8-12   [dl]
7.549 > Will install 8 system packages:
7.551 + git                   - remotes                 
7.551 + libcurl4-openssl-dev  - curl                    
7.551 + libicu-dev            - stringi                 
7.551 + libsasl2-dev          - mongolite               
7.551 + libssl-dev            - curl, mongolite, openssl
7.551 + libxml2-dev           - xml2                    
7.551 + pandoc                - knitr, rmarkdown        
7.551 + zlib1g-dev            - httpuv                  
7.680 i Getting 122 pkgs with unknown sizes
9.383 v Got askpass 1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (22.35 kB)
9.455 v Got anytime 0.3.9 (x86_64-pc-linux-gnu-ubuntu-22.04) (404.73 kB)
9.725 v Got actuar 3.3-2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.46 MB)
10.04 v Got crayon 1.5.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (158.60 kB)
10.08 v Got crul 1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (632.97 kB)
10.10 v Got callr 3.7.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (425.23 kB)
10.12 v Got cachem 1.0.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (65.82 kB)
10.16 v Got collections 0.3.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (67.62 kB)
10.25 v Got cyclocomp 1.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (30.42 kB)
10.30 v Got dygraphs 1.1.1.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (421.60 kB)
10.41 v Got digest 0.6.31 (x86_64-pc-linux-gnu-ubuntu-22.04) (197.23 kB)
10.43 v Got glue 1.6.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (146.46 kB)
10.52 v Got highr 0.10 (x86_64-pc-linux-gnu-ubuntu-22.04) (38.77 kB)
10.57 v Got httpcode 0.3.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (32.10 kB)
10.64 v Got evaluate 0.20 (x86_64-pc-linux-gnu-ubuntu-22.04) (77.52 kB)
10.76 v Got fontawesome 0.5.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.36 MB)
10.91 v Got dplyr 1.1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.45 MB)
11.04 v Got later 1.3.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (129.82 kB)
11.06 v Got htmltools 0.5.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (343.31 kB)
11.21 v Got jquerylib 0.1.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (526.59 kB)
11.35 v Got lazyeval 0.2.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (162.95 kB)
11.46 v Got memoise 2.0.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (47.54 kB)
11.54 v Got httr 1.4.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (497.68 kB)
11.55 v Got pkgload 1.3.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (173.40 kB)
11.65 v Got R.cache 0.16.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (108.01 kB)
11.80 v Got bslib 0.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.80 MB)
11.84 v Got mongolite 2.7.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (492.09 kB)
11.86 v Got reshape2 1.4.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (37.82 kB)
11.88 v Got lubridate 1.9.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (962.32 kB)
12.02 v Got pillar 1.9.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (644.48 kB)
12.08 v Got remotes 2.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (398.27 kB)
12.18 v Got processx 3.8.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (435.73 kB)
12.20 v Got knitr 1.42 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.44 MB)
12.30 v Got roxygen2 7.2.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (696.36 kB)
12.51 v Got shinydashboard 0.7.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (321.35 kB)
12.53 v Got styler 1.9.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (708.04 kB)
12.66 v Got R.utils 2.12.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.39 MB)
12.72 v Got tinytex 0.45 (x86_64-pc-linux-gnu-ubuntu-22.04) (132.53 kB)
12.79 v Got utf8 1.2.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (145.53 kB)
12.95 v Got tidyselect 1.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (219.41 kB)
13.13 v Got shinyWidgets 0.7.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.24 MB)
13.21 v Got tibble 3.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (672.06 kB)
13.27 v Got munsell 0.5.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (240.16 kB)
13.31 v Got ggradar 0.2 (source) (937.34 kB)
13.49 v Got urltools 1.7.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.98 MB)
13.61 v Got sass 0.4.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.41 MB)
13.69 v Got backports 1.4.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (99.76 kB)
13.79 v Got stringi 1.7.12 (x86_64-pc-linux-gnu-ubuntu-22.04) (3.22 MB)
13.88 v Got viridisLite 0.4.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.30 MB)
13.92 v Got fastmap 1.1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (61.80 kB)
13.95 v Got commonmark 1.9.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (146.72 kB)
14.03 v Got ghql 0.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (101.31 kB)
14.13 v Got desc 1.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (319.94 kB)
14.26 v Got farver 2.1.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.30 MB)
14.31 v Got cli 3.6.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.26 MB)
14.33 v Got curl 5.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (727.49 kB)
14.42 v Got expint 0.1-8 (x86_64-pc-linux-gnu-ubuntu-22.04) (210.94 kB)
14.50 v Got generics 0.1.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (73.20 kB)
14.57 v Got lifecycle 1.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (121.94 kB)
14.69 v Got jsonlite 1.8.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.09 MB)
14.77 v Got R.methodsS3 1.8.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (80.41 kB)
14.89 v Got ps 1.7.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (382.60 kB)
14.94 v Got ggplot2 3.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.28 MB)
14.96 v Got logger 0.2.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (776.22 kB)
15.07 v Got rex 1.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (122.98 kB)
15.08 v Got DT 0.27 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.61 MB)
15.10 v Got magrittr 2.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (232.13 kB)
15.12 v Got httpuv 1.6.9 (x86_64-pc-linux-gnu-ubuntu-22.04) (594.36 kB)
15.23 v Got stringr 1.5.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (299.60 kB)
15.24 v Got purrr 1.0.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (484.59 kB)
15.26 v Got timechange 0.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (182.03 kB)
15.32 v Got rappdirs 0.3.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (45.78 kB)
15.34 v Got withr 2.5.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (225.66 kB)
15.38 v Got labeling 0.4.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (58.42 kB)
15.51 v Got xmlparsedata 1.0.5 (x86_64-pc-linux-gnu-ubuntu-22.04) (18.36 kB)
15.56 v Got xml2 1.3.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (600.47 kB)
15.60 v Got forcats 1.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (422.49 kB)
15.61 v Got base64enc 0.1-3 (x86_64-pc-linux-gnu-ubuntu-22.04) (36.47 kB)
15.72 v Got xtable 1.8-4 (x86_64-pc-linux-gnu-ubuntu-22.04) (700.53 kB)
15.74 v Got yaml 2.3.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (111.24 kB)
15.75 v Got sourcetools 0.1.7-1 (x86_64-pc-linux-gnu-ubuntu-22.04) (45.95 kB)
15.79 v Got ellipsis 0.3.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (38.45 kB)
15.84 v Got xts 0.13.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (837.92 kB)
15.90 v Got rlang 1.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.54 MB)
15.96 v Got graphql 1.5.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (92.09 kB)
16.03 v Got config 0.3.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (79.95 kB)
16.14 v Got pkgconfig 2.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (17.51 kB)
16.21 v Got R6 2.5.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (82.45 kB)
16.38 v Got isoband 0.2.7 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.64 MB)
16.43 v Got htmlwidgets 1.6.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (811.99 kB)
16.45 v Got mime 0.12 (x86_64-pc-linux-gnu-ubuntu-22.04) (35.49 kB)
16.47 v Got rprojroot 2.0.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (101.42 kB)
16.54 v Got plyr 1.8.8 (x86_64-pc-linux-gnu-ubuntu-22.04) (820.75 kB)
16.64 v Got fs 1.6.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (284.42 kB)
16.70 v Got brew 1.0-8 (x86_64-pc-linux-gnu-ubuntu-22.04) (76.25 kB)
16.80 v Got crosstalk 1.2.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (403.98 kB)
16.81 v Got fansi 1.0.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (302.54 kB)
17.04 v Got tidyr 1.3.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.20 MB)
17.22 v Got lattice 0.21-8 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.34 MB)
17.53 v Got openssl 2.0.6 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.31 MB)
17.56 v Got Rcpp 1.0.10 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.12 MB)
17.77 v Got xfun 0.38 (x86_64-pc-linux-gnu-ubuntu-22.04) (414.98 kB)
17.99 v Got Matrix 1.5-4 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.64 MB)
18.01 v Got zoo 1.8-12 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.01 MB)
18.07 v Got here 1.0.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (52.30 kB)
18.21 v Got colorspace 2.1-0 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.59 MB)
18.26 v Got golem 0.4.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.14 MB)
18.33 v Got attempt 0.3.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (106.98 kB)
18.35 v Got scales 1.2.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (607.90 kB)
18.45 v Got triebeard 0.4.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (189.42 kB)
18.55 v Got languageserver 0.3.15 (x86_64-pc-linux-gnu-ubuntu-22.04) (813.51 kB)
18.59 v Got RColorBrewer 1.1-3 (x86_64-pc-linux-gnu-ubuntu-22.04) (53.06 kB)
18.76 v Got lintr 3.0.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.04 MB)
18.98 v Got rmarkdown 2.21 (x86_64-pc-linux-gnu-ubuntu-22.04) (2.56 MB)
19.05 v Got vctrs 0.6.2 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.28 MB)
19.08 v Got R.oo 1.25.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (954.78 kB)
19.12 v Got rlog 0.1.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (15.49 kB)
19.23 v Got promises 1.2.0.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.94 MB)
19.28 v Got gtable 0.3.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (214.22 kB)
19.30 v Got sys 3.4.1 (x86_64-pc-linux-gnu-ubuntu-22.04) (53.79 kB)
19.38 v Got MASS 7.3-58.3 (x86_64-pc-linux-gnu-ubuntu-22.04) (1.12 MB)
19.98 v Got shiny 1.7.4 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.24 MB)
20.02 i Installing system requirements
20.03 i Executing `sh -c apt-get -y update`
25.15 i Executing `sh -c apt-get -y install libcurl4-openssl-dev libssl-dev zlib1g-dev pandoc libsasl2-dev git libicu-dev libxml2-dev`
34.45 v Installed actuar 3.3-2  (90ms)
34.52 v Installed anytime 0.3.9  (117ms)
34.54 v Installed askpass 1.1  (173ms)
34.56 v Installed attempt 0.3.1  (191ms)
34.60 v Installed backports 1.4.1  (220ms)
34.65 v Installed base64enc 0.1-3  (241ms)
34.68 v Installed brew 1.0-8  (281ms)
34.71 v Installed bslib 0.4.2  (300ms)
34.73 v Installed cachem 1.0.7  (319ms)
34.77 v Installed callr 3.7.3  (336ms)
34.81 v Installed cli 3.6.1  (228ms)
34.86 v Installed collections 0.3.7  (62ms)
34.89 v Installed commonmark 1.9.0  (58ms)
34.96 v Installed config 0.3.1  (54ms)
35.00 v Installed crayon 1.5.2  (84ms)
35.05 v Installed crosstalk 1.2.0  (62ms)
35.09 v Installed crul 1.3  (60ms)
36.13 v Installed curl 5.0.0  (1.1s)
36.18 v Installed cyclocomp 1.1.0  (1.1s)
36.22 v Installed desc 1.4.2  (64ms)
36.29 v Installed digest 0.6.31  (64ms)
36.35 v Installed dplyr 1.1.1  (100ms)
37.41 v Installed DT 0.27  (1.1s)
37.45 v Installed dygraphs 1.1.1.6  (1.1s)
37.49 v Installed ellipsis 0.3.2  (60ms)
37.56 v Installed evaluate 0.20  (57ms)
37.61 v Installed expint 0.1-8  (94ms)
37.66 v Installed fansi 1.0.4  (77ms)
37.70 v Installed fastmap 1.1.1  (58ms)
38.74 v Installed fontawesome 0.5.1  (1.1s)
38.78 v Installed fs 1.6.1  (1.1s)
38.82 v Installed generics 0.1.3  (57ms)
38.87 v Installed ghql 0.1.0  (70ms)
38.91 v Installed glue 1.6.2  (74ms)
40.04 v Installed golem 0.4.0  (1.1s)
40.07 v Installed graphql 1.5.1  (1.1s)
40.13 v Installed here 1.0.1  (56ms)
40.16 v Installed highr 0.10  (69ms)
40.21 v Installed htmltools 0.5.5  (57ms)
41.25 v Installed htmlwidgets 1.6.2  (1.1s)
41.28 v Installed httpcode 0.3.0  (1.1s)
42.33 v Installed httpuv 1.6.9  (1.1s)
42.38 v Installed httr 1.4.5  (1.1s)
42.42 v Installed jquerylib 0.1.4  (73ms)
43.48 v Installed jsonlite 1.8.4  (1.1s)
43.53 v Installed knitr 1.42  (1.1s)
43.57 v Installed languageserver 0.3.15  (70ms)
43.61 v Installed later 1.3.0  (56ms)
44.66 v Installed lattice 0.21-8  (1.1s)
44.70 v Installed lazyeval 0.2.2  (1.1s)
44.74 v Installed lifecycle 1.0.3  (58ms)
45.78 v Installed lintr 3.0.2  (1.1s)
45.84 v Installed logger 0.2.2  (1.1s)
45.89 v Installed lubridate 1.9.2  (80ms)
45.93 v Installed magrittr 2.0.3  (60ms)
45.97 v Installed memoise 2.0.1  (56ms)
46.01 v Installed mime 0.12  (56ms)
47.05 v Installed mongolite 2.7.2  (1.1s)
47.09 v Installed openssl 2.0.6  (1.1s)
48.13 v Installed pillar 1.9.0  (1.1s)
48.17 v Installed pkgconfig 2.0.3  (1.1s)
48.21 v Installed pkgload 1.3.2  (57ms)
48.25 v Installed plyr 1.8.8  (61ms)
48.32 v Installed processx 3.8.1  (80ms)
48.36 v Installed promises 1.2.0.1  (81ms)
48.40 v Installed ps 1.7.5  (61ms)
48.44 v Installed purrr 1.0.1  (60ms)
48.48 v Installed R.cache 0.16.0  (60ms)
48.54 v Installed R.methodsS3 1.8.2  (74ms)
48.58 v Installed R.oo 1.25.0  (73ms)
49.64 v Installed R.utils 2.12.2  (1.1s)
49.68 v Installed R6 2.5.1  (1.1s)
49.72 v Installed rappdirs 0.3.3  (57ms)
50.79 v Installed Rcpp 1.0.10  (1.1s)
50.83 v Installed remotes 2.4.2  (1.1s)
52.92 Error: 
52.92 ! error in pak subprocess
52.92 Caused by error in `verify_extracted_package(filename, pkg_cache)`:
52.92 ! 
52.92 '/tmp/Rtmppd6cZo/file1d576916aa/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.2/reshape2_1.4.4.tar.gz'
52.92 is not a valid binary, it is missing reshape2/Meta/package.rds.
52.92 ---
52.92 Backtrace:
52.92 1. pak::pak()
52.92 2. pak::local_install_dev_deps(...)
52.92 3. pak:::remote(function(...) { ...
52.92 4. err$throw(res$error)
52.92 ---
52.92 Subprocess backtrace:
52.92  1. base::withCallingHandlers(cli_message = function(msg) { ...
52.92  2. get("local_install_dev_deps_do_plan", asNamespace("pak"))(...)
52.92  3. pak:::pkg_install_do_plan(proposal = NULL)
52.92  4. proposal$install()
52.92  5. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, ...
52.92  6. base::withCallingHandlers({ ...
52.92  7. pkgdepends:::handle_events(state, events)
52.92  8. pkgdepends:::handle_event(state, i)
52.92  9. proc$get_result()
52.92 10. processx:::process_get_result(self, private)
52.92 11. private$post_process()
52.92 12. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, ...
52.92 13. pkgdepends:::verify_extracted_package(filename, pkg_cache)
52.92 14. base::throw(pkg_error("{.path {filename}} is not a valid binary, it is missing...
52.92 15. | base::signalCondition(cond)
52.92 16. global (function (e) ...
52.92 Execution halted

Like @Jondeen - I'm seeing a decent failure rate, I'm just looping the docker build on my laptop with --no-cache flags to force it to happen and I'm seeing a failure rate of 12 out of the last 15 builds I tried.

@gaborcsardi
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@danielloader That does not look like CRAN, looks like PPM. What's the output of this?

getOption("repos")

@gaborcsardi
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gaborcsardi commented Aug 1, 2024 •
edited
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I have a very vague guess. Can you set this env var, right after you start R, i.e. before loading pak?

Sys.setenv("PKGCACHE_HTTP_VERSION" = "2")

EDIT: never mind, this is something else.

@gaborcsardi
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I believe that this was already fixed by dev pak (pkgcache) here:
r-lib/pkgcache@bee4e93

Latest pak release:

> pak::meta_list("reshape2")[["sources"]]
[[1]]
[1] "https://p3m.dev/cran/__linux__/jammy/2024-02-28/src/contrib/reshape2_1.4.4.tar.gz"
[2] "https://p3m.dev/cran/__linux__/jammy/2024-02-28/src/contrib/Archive/reshape2/reshape2_1.4.4.tar.gz"

Dev pak:

> pak::meta_list("reshape2")[["sources"]]
[[1]]
[1] "https://p3m.dev/cran/__linux__/jammy/2024-02-28/src/contrib/reshape2_1.4.4.tar.gz"

If you use a pak nightly build from https://pak.r-lib.org/reference/install.html#nightly-builds then it should happen.

@danielloader
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Not to pester but is there likely to be a promotion of these nightly builds into a production build? Else I've got to update many dozens of dockerfiles to change the build step rather than just using latest stable.

@gaborcsardi
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It should not happen any more with pak 0.8.0:

> getOption("repos")
                                                          P3M
"https://packagemanager.posit.co/cran/__linux__/jammy/latest"
                                                         CRAN
                                "https://cloud.r-project.org"
> pak::meta_list("reshape2")[["sources"]]
[[1]]
[1] "https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/reshape2_1.4.4.tar.gz"

[[2]]
[1] "https://cloud.r-project.org/src/contrib/reshape2_1.4.4.tar.gz"
[2] "https://cloud.r-project.org/src/contrib/Archive/reshape2/reshape2_1.4.4.tar.gz"

@martinmodrak
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martinmodrak commented Dec 10, 2024 •
edited
Loading

I'll just note that I am seeing the same problem when using pak with renv. Not completely sure what's happening as the renv layer adds extra problems.

Just in case this is helpful an example is installing the ps package version 1.8.1

Error:                                                                                                                                                                              
! error in pak subprocess
Caused by error in `verify_extracted_package(filename, pkg_cache)`:
! /tmp/Rtmp3T9klN/fileb7973372942d/src/contrib/ps_1.7.6-927a2deb59.tar.gz is not a valid binary, it is missing ps/Meta/package.rds.

The sources are:

pak::meta_list("ps")[["sources"]]
# [[1]]
# [1] "https://cloud.r-project.org/src/contrib/ps_1.8.1.tar.gz"            "https://cloud.r-project.org/src/contrib/Archive/ps/ps_1.8.1.tar.gz"

The tar.gz seems to be just a source archive, but pak is trying to treat it as a binary package.

Directly running pak::pkg_install("[email protected]") installs without problems....

Thanks for the great package and sorry for not having a complete repro (I in no way insist on you investigating or fixing this soon, just hope it helps others with the same error message to maybe provide more info).

I am using pak 0.8.0

@martinmodrak
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Update: I have a repro - it seems at least some old versions cause problems:

pak::pkg_install("[email protected]")

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@gaborcsardi @Jondeen @danielloader @martinmodrak