Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-02-26 14:01:57 -0500 (Mon, 26 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 272/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.37.0  (landing page)
David Rossell
Snapshot Date: 2024-02-23 14:00:08 -0500 (Fri, 23 Feb 2024)
git_url: https://git.bioconductor.org/packages/casper
git_branch: devel
git_last_commit: fdb9dd6
git_last_commit_date: 2023-10-24 09:52:32 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for casper on kunpeng2


To the developers/maintainers of the casper package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/casper.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: casper
Version: 2.37.0
Command: /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings casper_2.37.0.tar.gz
StartedAt: 2024-02-24 04:33:32 -0000 (Sat, 24 Feb 2024)
EndedAt: 2024-02-24 04:39:55 -0000 (Sat, 24 Feb 2024)
EllapsedTime: 383.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: casper.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings casper_2.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/casper.Rcheck’
* using R Under development (unstable) (2024-01-16 r85812)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.37.0’
* 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 ‘casper’ can be installed ... WARNING
Found the following significant warnings:
  model.cpp:147:10: warning: ‘sprintf’ argument 3 overlaps destination object ‘<unknown>’ [-Wrestrict]
  variant.cpp:164:45: warning: ‘sprintf’ argument 3 overlaps destination object ‘str’ [-Wrestrict]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/casper.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.4Mb
* 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
File ‘casper/libs/casper.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Objects: ‘fragFunc.o’, ‘hash.o’, ‘join_exons.o’, ‘makeIslands.o’,
      ‘model.o’, ‘pathCounts.o’, ‘procBam.o’, ‘simReads.o’,
      ‘simReadsfunc.o’, ‘uniqQname.o’, ‘variant.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/casper.Rcheck/00check.log’
for details.



Installation output

casper.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD INSTALL casper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library’
* installing *source* package ‘casper’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c casper.cpp -o casper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c cstat.cpp -o cstat.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c dataframe.cpp -o dataframe.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c discretedf.cpp -o discretedf.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c dropVariant.cpp -o dropVariant.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c exon.cpp -o exon.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c fragment.cpp -o fragment.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c functions.c -o functions.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c join_exons.c -o join_exons.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c model.cpp -o model.o
model.cpp: In member function ‘char* Model::toString()’:
model.cpp:147:10: warning: ‘sprintf’ argument 3 overlaps destination object ‘<unknown>’ [-Wrestrict]
  147 |   sprintf(str, "%s {%s}", str, vstr);
      |   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c model_cmp.cpp -o model_cmp.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c procBam.c -o procBam.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c rcasper.cpp -o rcasper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c seppel.cpp -o seppel.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c variant.cpp -o variant.o
variant.cpp: In member function ‘void Variant::toString(char*)’:
variant.cpp:164:45: warning: ‘sprintf’ argument 3 overlaps destination object ‘str’ [-Wrestrict]
  164 |  for (int e = 0; e < exonCount; e++) sprintf(str, "%s,%i", str, exons[e]->id);
      |                                      ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
variant.cpp:156:30: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here
  156 | void Variant::toString(char *str)
      |                        ~~~~~~^~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel_2024-01-16_r85812/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c variant_cmp.cpp -o variant_cmp.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-devel_2024-01-16_r85812/lib -L/usr/local/lib -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -L/home/biocbuild/R/R-devel_2024-01-16_r85812/lib -lR
installing to /home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/00LOCK-casper/00new/casper/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘transcripts’ in package ‘casper’
** 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 (casper)

Tests output


Example timings

casper.Rcheck/casper-Ex.timings

nameusersystemelapsed
K562.r1l10.1810.0010.182
annotatedGenome-class0.0010.0000.001
asymmetryCheck0.0160.0000.016
calcDenovo000
calcExp3.8450.0513.904
denovoExpr3.9370.0844.028
denovoGeneExpr-class0.0000.0000.001
denovoGenomeExpr-class000
distrsGSE377040.1460.0040.150
genePlot0.3760.0040.380
getDistrs0.5170.0000.518
getIsland0.1240.0000.125
getNreads000
getReads000
getRoc000
hg19DB0.1250.0000.126
mergeBatches0.1170.0000.117
mergeExp0.0010.0000.000
modelPrior0.4900.0000.492
modelPriorAS-class0.0010.0000.000
pathCounts-class000
pathCounts000
plot-methods000
plotExpr000
plotPriorAS000
probNonEquiv0.1270.0000.127
procBam-class0.0000.0000.001
procBam000
procGenome000
qqnormGenomeWide0.0750.0000.075
quantileNorm0.0140.0000.015
relexprByGene000
rmShortInserts000
simMAE0.0000.0000.001
simMAEcheck000
simMultSamples000
simReads0.5070.0060.514
simulatedSamples-class0.0010.0000.001
splitGenomeByLength000
transcripts0.2360.0040.241
wrapDenovo000
wrapKnown000