| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-29 16:34:05 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the PharmacoGx package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PharmacoGx.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1456/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PharmacoGx 3.3.2 (landing page) Benjamin Haibe-Kains
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: PharmacoGx |
| Version: 3.3.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PharmacoGx_3.3.2.tar.gz |
| StartedAt: 2023-01-29 06:03:16 -0000 (Sun, 29 Jan 2023) |
| EndedAt: 2023-01-29 06:24:21 -0000 (Sun, 29 Jan 2023) |
| EllapsedTime: 1265.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: PharmacoGx.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PharmacoGx_3.3.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PharmacoGx.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘3.3.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PharmacoGx’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'PharmacoGx' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... WARNING
Error in library(PharmacoGx, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘PharmacoGx’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.Hill’ ‘.summarizeSensitivityNumbers’ ‘partialCorQUICKSTOP’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Killed
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 2251 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘CreatingPharmacoSet.Rmd’ using ‘UTF-8’... OK
‘DetectingDrugSynergyAndAntagonism.Rmd’ using ‘UTF-8’... OK
‘PharmacoGx.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘CreatingPharmacoSet.Rmd’ using rmarkdown
--- finished re-building ‘CreatingPharmacoSet.Rmd’
--- re-building ‘DetectingDrugSynergyAndAntagonism.Rmd’ using rmarkdown
Killed
--- re-building ‘PharmacoGx.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PharmacoGx.Rcheck/vign_test/PharmacoGx/vignettes/PharmacoGx_files/figure-html/fig1-1.png" but not available.
--- finished re-building ‘PharmacoGx.Rmd’
SUMMARY: processing the following file failed:
‘DetectingDrugSynergyAndAntagonism.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/PharmacoGx.Rcheck/00check.log’
for details.
PharmacoGx.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PharmacoGx
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘PharmacoGx’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c metaPermC.c -o metaPermC.o
metaPermC.c: In function ‘runPerm’:
metaPermC.c:143:12: warning: unused variable ‘num_larger’ [-Wunused-variable]
143 | uint64_t num_larger = 0;
| ^~~~~~~~~~
metaPermC.c: In function ‘partialCorQUICKSTOP’:
metaPermC.c:328:10: warning: unused variable ‘temp’ [-Wunused-variable]
328 | double temp;
| ^~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rCPP_bridge.cpp -o rCPP_bridge.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o PharmacoGx.so RcppExports.o metaPermC.o rCPP_bridge.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-PharmacoGx/00new/PharmacoGx/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PharmacoGx)
PharmacoGx.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.unsetenv("R_TESTS")
>
> library(testthat)
> library(PharmacoGx)
Loading required package: CoreGx
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'PharmacoGx'
The following objects are masked from 'package:CoreGx':
.parseToRoxygen, amcc, connectivityScore, cosinePerm, gwc, mcc
>
> test_check("PharmacoGx")
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lower_bounds 0 0 0
upper_bounds 1 1 -1
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[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 3 | SKIP 1 | PASS 129 ]
>
> proc.time()
user system elapsed
97.016 0.964 109.484