Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-20 12:05:05 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for casper on nebbiolo1


To the developers/maintainers of the casper package:
- Please 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 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.

raw results

Package 254/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.30.0  (landing page)
David Rossell
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/casper
git_branch: RELEASE_3_15
git_last_commit: 140c9ad
git_last_commit_date: 2022-04-26 11:13:19 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: casper
Version: 2.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings casper_2.30.0.tar.gz
StartedAt: 2022-05-19 18:40:57 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 18:45:22 -0400 (Thu, 19 May 2022)
EllapsedTime: 265.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: casper.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings casper_2.30.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/casper.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.30.0’
* 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:147:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  variant.cpp:164:77: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See ‘/home/biocbuild/bbs-3.15-bioc/meat/casper.Rcheck/00install.out’ for details.
* 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 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 ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/casper.Rcheck/00check.log’
for details.



Installation output

casper.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL casper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘casper’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c casper.cpp -o casper.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cstat.cpp -o cstat.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dataframe.cpp -o dataframe.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c discretedf.cpp -o discretedf.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dropVariant.cpp -o dropVariant.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c exon.cpp -o exon.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fragment.cpp -o fragment.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c functions.c -o functions.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c join_exons.c -o join_exons.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/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:147:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  147 |   sprintf(str, "%s {%s}", str, vstr);
      |                                    ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c model_cmp.cpp -o model_cmp.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c procBam.c -o procBam.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rcasper.cpp -o rcasper.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c seppel.cpp -o seppel.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/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:164:77: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  164 |  for (int e = 0; e < exonCount; e++) sprintf(str, "%s,%i", str, exons[e]->id);
      |                                                                             ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c variant_cmp.cpp -o variant_cmp.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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.r1l10.1580.0000.158
annotatedGenome-class0.0020.0000.002
asymmetryCheck0.0130.0000.014
calcDenovo0.0000.0000.001
calcExp3.290.183.47
denovoExpr2.8370.1562.993
denovoGeneExpr-class0.0020.0000.001
denovoGenomeExpr-class0.0010.0000.000
distrsGSE377040.1500.0040.153
genePlot0.2730.0040.277
getDistrs0.3850.0000.384
getIsland0.1140.0000.114
getNreads0.0010.0000.000
getReads000
getRoc0.0000.0000.001
hg19DB0.1130.0040.117
mergeBatches0.0820.0000.082
mergeExp000
modelPrior0.3430.0040.348
modelPriorAS-class0.0010.0000.000
pathCounts-class0.0010.0000.000
pathCounts0.0010.0000.000
plot-methods000
plotExpr0.0000.0000.001
plotPriorAS000
probNonEquiv0.1210.0160.136
procBam-class0.0010.0000.000
procBam0.0010.0000.000
procGenome0.0010.0000.000
qqnormGenomeWide0.0440.0000.044
quantileNorm0.0140.0000.014
relexprByGene000
rmShortInserts0.0000.0000.001
simMAE000
simMAEcheck0.0000.0010.000
simMultSamples000
simReads0.4150.0080.422
simulatedSamples-class0.0000.0010.001
splitGenomeByLength000
transcripts0.1820.0010.183
wrapDenovo0.0000.0000.001
wrapKnown000