Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-17 11:06:56 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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? here 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 245/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.29.1  (landing page)
David Rossell
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/casper
git_branch: master
git_last_commit: ff4be92
git_last_commit_date: 2021-11-20 23:20:07 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: casper
Version: 2.29.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:casper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings casper_2.29.1.tar.gz
StartedAt: 2022-01-16 18:30:51 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 18:34:58 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 247.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: casper.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:casper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings casper_2.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/casper.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'casper/DESCRIPTION' ... OK
* this is package 'casper' version '2.29.1'
* 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 whether package 'casper' can be installed ... WARNING
Found the following significant warnings:
  model.cpp:147:11: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  variant.cpp:164:46: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'D:/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
  'D:/biocbuild/bbs-3.15-bioc/meat/casper.Rcheck/00check.log'
for details.



Installation output

casper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL casper
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'casper' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c casper.cpp -o casper.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cstat.cpp -o cstat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dataframe.cpp -o dataframe.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c discretedf.cpp -o discretedf.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dropVariant.cpp -o dropVariant.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c exon.cpp -o exon.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fragFunc.c -o fragFunc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fragment.cpp -o fragment.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c functions.c -o functions.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c hash.c -o hash.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c join_exons.c -o join_exons.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c makeIslands.c -o makeIslands.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c model.cpp -o model.o
model.cpp: In member function 'char* Model::toString()':
model.cpp:147:11: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
   sprintf(str, "%s {%s}", str, vstr);
           ^~~             ~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c model_cmp.cpp -o model_cmp.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c pathCounts.c -o pathCounts.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c procBam.c -o procBam.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rcasper.cpp -o rcasper.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c seppel.cpp -o seppel.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c simReads.c -o simReads.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c simReadsfunc.c -o simReadsfunc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c smartmodeldist.cpp -o smartmodeldist.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c uniqQname.c -o uniqQname.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c variant.cpp -o variant.o
variant.cpp: In member function 'void Variant::toString(char*)':
variant.cpp:164:46: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  for (int e = 0; e < exonCount; e++) sprintf(str, "%s,%i", str, exons[e]->id);
                                              ^~~           ~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c variant_cmp.cpp -o variant_cmp.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o casper.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-casper/00new/casper/libs/x64
** 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
  converting help for package 'casper'
    finding HTML links ... done
    K562.r1l1                               html  
    annotatedGenome-class                   html  
    asymmetryCheck                          html  
    calcDenovo                              html  
    calcExp                                 html  
    denovoExpr                              html  
    denovoGeneExpr-class                    html  
    denovoGenomeExpr-class                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-casper/00new/casper/help/denovoGeneExpr-class.html
    distrsGSE37704                          html  
    genePlot                                html  
    getDistrs                               html  
    getIsland                               html  
    getNreads                               html  
    getReads                                html  
    getRoc                                  html  
    hg19DB                                  html  
    mergeBatches                            html  
    mergeExp                                html  
    modelPrior                              html  
    modelPriorAS-class                      html  
    pathCounts-class                        html  
    pathCounts                              html  
    plot-methods                            html  
    plotExpr                                html  
    plotPriorAS                             html  
    probNonEquiv                            html  
    procBam-class                           html  
    procBam                                 html  
    procGenome                              html  
    qqnormGenomeWide                        html  
    quantileNorm                            html  
    relexprByGene                           html  
    rmShortInserts                          html  
    simMAE                                  html  
    simMAEcheck                             html  
    simMultSamples                          html  
    simReads                                html  
    simulatedSamples-class                  html  
    splitGenomeByLength                     html  
    subsetGenome                            html  
    transcripts                             html  
    txLength-methods                        html  
    wrapDenovo                              html  
    wrapKnown                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (casper)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'plotgardener' is missing or broken
 done

Tests output


Example timings

casper.Rcheck/casper-Ex.timings

nameusersystemelapsed
K562.r1l10.150.030.19
annotatedGenome-class000
asymmetryCheck000
calcDenovo000
calcExp2.370.813.19
denovoExpr3.080.984.06
denovoGeneExpr-class000
denovoGenomeExpr-class000
distrsGSE377040.130.040.16
genePlot0.310.010.38
getDistrs0.450.110.56
getIsland0.090.030.12
getNreads000
getReads000
getRoc000
hg19DB0.140.000.14
mergeBatches0.090.000.09
mergeExp000
modelPrior0.400.050.44
modelPriorAS-class000
pathCounts-class000
pathCounts000
plot-methods000
plotExpr000
plotPriorAS000
probNonEquiv0.110.000.11
procBam-class000
procBam000
procGenome000
qqnormGenomeWide0.060.000.06
quantileNorm0.020.000.01
relexprByGene000
rmShortInserts000
simMAE000
simMAEcheck000
simMultSamples000
simReads0.480.130.61
simulatedSamples-class000
splitGenomeByLength000
transcripts0.160.000.15
wrapDenovo000
wrapKnown000