| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:07 -0000 (Wed, 08 Feb 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" | 4164 |
| 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 GSVA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSVA.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 865/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GSVA 1.47.0 (landing page) Robert Castelo
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: GSVA |
| Version: 1.47.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GSVA_1.47.0.tar.gz |
| StartedAt: 2023-02-07 03:58:59 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 04:08:38 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 579.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GSVA.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GSVA_1.47.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GSVA.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 ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘1.47.0’
* package encoding: latin1
* 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 ‘GSVA’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* 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 ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘GSVA.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘GSVA.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/GSVA.Rcheck/vign_test/GSVA/vignettes/GSVA_files/figure-html/compcorrs-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/GSVA.Rcheck/vign_test/GSVA/vignettes/GSVA_files/figure-html/compsexgenesets-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/GSVA.Rcheck/vign_test/GSVA/vignettes/GSVA_files/figure-html/gbmSignature-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/GSVA.Rcheck/vign_test/GSVA/vignettes/GSVA_files/figure-html/leukemiavolcano-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/GSVA.Rcheck/vign_test/GSVA/vignettes/GSVA_files/figure-html/leukemiaheatmap-1.png" but not available.
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/GSVA.Rcheck/00check.log’
for details.
GSVA.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GSVA
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘GSVA’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c ks_test.c -o ks_test.o
ks_test.c: In function ‘ks_sample’:
ks_test.c:24:16: warning: unused variable ‘mx_value’ [-Wunused-variable]
24 | double mx_value = 0.0;
| ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c register_cmethods.c -o register_cmethods.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-GSVA/00new/GSVA/libs
** R
** 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 (GSVA)
GSVA.Rcheck/tests/runTests.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.
> BiocGenerics:::testPackage("GSVA")
Estimating PLAGE scores for 2 gene sets.
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Estimating PLAGE scores for 2 gene sets.
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Estimating combined z-scores for 2 gene sets.
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Estimating ssGSEA scores for 2 gene sets.
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Estimating ssGSEA scores for 2 gene sets.
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Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels
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Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels
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Estimating PLAGE scores for 2 gene sets.
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expression data. In order to take advantage of the sparse Matrix type, the scaling
will only be applied to the non-zero values of the data. This is a provisional
solution in order to give support to the dgCMatrix format.
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Estimating combined z-scores for 2 gene sets.
Please bear in mind that this method first scales the values of the gene
expression data. In order to take advantage of the sparse Matrix type, the scaling
will only be applied to the non-zero values of the data. This is a provisional
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Estimating ssGSEA scores for 2 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
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[1] "Normalizing..."
Estimating ssGSEA scores for 2 gene sets.
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[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
RUNIT TEST PROTOCOL -- Tue Feb 7 04:04:27 2023
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
GSVA RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
There were 13 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
29.759 0.977 33.430
GSVA.Rcheck/GSVA-Ex.timings
| name | user | system | elapsed | |
| computeGeneSetsOverlap | 0.062 | 0.008 | 0.085 | |
| filterGeneSets | 0.001 | 0.000 | 0.001 | |
| gsva | 0.367 | 0.036 | 0.403 | |
| igsva | 0.001 | 0.000 | 0.000 | |