Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-09-21 11:40:32 -0400 (Thu, 21 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4654
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4388
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4402
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4391
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

Package 343/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.23.0  (landing page)
Alicia Schep
Snapshot Date: 2023-09-20 14:05:05 -0400 (Wed, 20 Sep 2023)
git_url: https://git.bioconductor.org/packages/chromVAR
git_branch: devel
git_last_commit: de4dcab
git_last_commit_date: 2023-04-25 10:57:03 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for chromVAR on kunpeng2


To the developers/maintainers of the chromVAR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromVAR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: chromVAR
Version: 1.23.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings chromVAR_1.23.0.tar.gz
StartedAt: 2023-09-21 02:47:22 -0000 (Thu, 21 Sep 2023)
EndedAt: 2023-09-21 02:58:48 -0000 (Thu, 21 Sep 2023)
EllapsedTime: 686.2 seconds
RetCode: 0
Status:   OK  
CheckDir: chromVAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings chromVAR_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/chromVAR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ version ‘1.23.0’
* 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 ‘chromVAR’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
* 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 loading without being on the library search path ... 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 ... NOTE
left_right_to_grglist: no visible global function definition for
  ‘GenomicRangesList’
Undefined global functions or variables:
  GenomicRangesList
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
deviationsCovariability 46.624  0.475  47.193
getJasparMotifs          7.541  0.336   7.891
pwmDistance              7.434  0.183   7.635
computeDeviations        7.200  0.140   7.354
plotVariability          5.237  0.060   5.306
computeVariability       5.176  0.100   5.288
* 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 ...
  ‘Introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/chromVAR.Rcheck/00check.log’
for details.



Installation output

chromVAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL chromVAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c pwm_similarity.cpp -o pwm_similarity.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘Rcpp::NumericVector row_sds(arma::mat&, bool)’:
utils.cpp:12:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   12 |     for( int j=0; j < X.n_rows; j++ ) {
      |                   ~~^~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-chromVAR/00new/chromVAR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (chromVAR)

Tests output

chromVAR.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.

> library(testthat)
> library(chromVAR)

> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
 30.514   1.849  32.394 

Example timings

chromVAR.Rcheck/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias0.8190.0480.870
annotationMatches0.0140.0040.018
chromVAR_theme0.1380.0040.143
computeDeviations7.2000.1407.354
computeExpectations0.0330.0000.033
computeVariability5.1760.1005.288
counts0.010.000.01
deviationScores0.0070.0000.007
deviations0.0070.0000.007
deviationsCovariability46.624 0.47547.193
deviationsTsne0.0860.0000.086
differentialDeviations0.0150.0000.014
differentialVariability0.0310.0000.031
example_counts0.0010.0000.001
filterPeaks0.3040.0040.308
filterSamples0.0610.0080.069
filterSamplesPlot0.1620.0000.163
getAnnotations0.4570.0040.462
getBackgroundPeaks0.6670.0720.741
getCisGroups0.1270.0000.128
getCounts4.2000.6824.895
getFragmentsPerPeak0.0120.0000.012
getFragmentsPerSample0.0110.0000.012
getJasparMotifs7.5410.3367.891
getPeaks0.1640.0160.178
getPermutedData1.3400.1711.515
getSampleCorrelation0.0190.0000.019
getSampleDepths0.1830.0480.231
getSampleDistance0.020.000.02
getTotalFragments0.0120.0000.011
makeBiasBins0.0670.0000.067
makePermutedSets1.2730.1121.390
matchKmers1.4010.1041.508
mini_counts0.0010.0000.001
mini_dev0.0010.0000.001
mini_ix0.0010.0000.001
plotVariability5.2370.0605.306
pwmDistance7.4340.1837.635
rbind-chromVARDeviations-method0.0670.0160.084