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BioC 3.5: CHECK report for casper on veracruz2

This page was generated on 2017-08-16 13:30:46 -0400 (Wed, 16 Aug 2017).

Package 174/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.10.0
David Rossell
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/casper
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: casper
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings casper_2.10.0.tar.gz
StartedAt: 2017-08-16 00:38:15 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:42:39 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 263.8 seconds
RetCode: 0
Status:  OK 
CheckDir: casper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings casper_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/casper.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.10.0’
* 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 ... OK
* 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 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
.mergeFramesViaRanges: no visible global function definition for
  ‘queryHits’
.mergeFramesViaRanges: no visible global function definition for
  ‘subjectHits’
assignExons2GeneF: no visible global function definition for
  ‘queryHits’
assignExons2GeneF: no visible global function definition for
  ‘subjectHits’
findNewExonsF: no visible global function definition for ‘queryHits’
generateNOexons: no visible global function definition for ‘queryHits’
generateNOexons: no visible global function definition for
  ‘subjectHits’
getDistrsFromBam: no visible global function definition for
  ‘subjectHits’
getDistrsFromBam: no visible global function definition for ‘queryHits’
getDistrsFrompBam: no visible global function definition for
  ‘subjectHits’
getDistrsFrompBam: no visible global function definition for
  ‘queryHits’
procPaths: no visible global function definition for ‘queryHits’
procPaths: no visible global function definition for ‘subjectHits’
Undefined global functions or variables:
  queryHits subjectHits
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
denovoExpr 5.49  0.307   5.981
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/casper.Rcheck/00check.log’
for details.


casper.Rcheck/00install.out:

* installing *source* package ‘casper’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c casper.cpp -o casper.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cstat.cpp -o cstat.o
cstat.cpp:16:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
static const char interface_c_sccs_id[] = "%W%";
                  ^
cstat.cpp:17:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
static const char mess_c_sccs_id[] = "%W%";
                  ^
cstat.cpp:18:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
static const char nrutil_c_sccs_id[] = "%W%"; 
                  ^
cstat.cpp:19:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
static const char vector_c_sccs_id[] = "%W%";
                  ^
cstat.cpp:20:19: warning: unused variable 'rand_c_sccs_id' [-Wunused-const-variable]
static const char rand_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
                  ^
cstat.cpp:21:19: warning: unused variable 'cstat_c_sccs_id' [-Wunused-const-variable]
static const char cstat_c_sccs_id[] = "@(#)$Workfile: cstat.c$ $Revision: 2011-08-23$";
                  ^
6 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dataframe.cpp -o dataframe.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c discretedf.cpp -o discretedf.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dropVariant.cpp -o dropVariant.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c exon.cpp -o exon.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fragFunc.c -o fragFunc.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fragment.cpp -o fragment.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c functions.c -o functions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hash.c -o hash.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c join_exons.c -o join_exons.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c makeIslands.c -o makeIslands.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c model.cpp -o model.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c model_cmp.cpp -o model_cmp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pathCounts.c -o pathCounts.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c procBam.c -o procBam.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rcasper.cpp -o rcasper.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c seppel.cpp -o seppel.o
seppel.cpp:484:2: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]
        delete [] possiblemodels;
        ^     ˜˜˜
seppel.cpp:402:36: note: allocated with 'new' here
  vector<Model*>* possiblemodels = new vector<Model*>();
                                   ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c simReads.c -o simReads.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c simReadsfunc.c -o simReadsfunc.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c smartmodeldist.cpp -o smartmodeldist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c uniqQname.c -o uniqQname.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c variant.cpp -o variant.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c variant_cmp.cpp -o variant_cmp.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/casper.Rcheck/casper/libs
** R
** data
** inst
** preparing 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
* DONE (casper)

casper.Rcheck/casper-Ex.timings:

nameusersystemelapsed
K562.r1l10.2090.0050.225
annotatedGenome-class0.0010.0010.001
asymmetryCheck0.0760.0130.089
calcDenovo0.0010.0000.000
calcExp2.7710.2993.188
denovoExpr5.4900.3075.981
denovoGeneExpr-class0.0010.0000.001
denovoGenomeExpr-class000
distrsGSE377040.1800.0050.188
genePlot0.4330.0030.456
getDistrs0.3830.0090.407
getIsland0.0870.0020.099
getNreads0.0010.0000.000
getReads0.0010.0000.000
getRoc0.0010.0000.000
hg19DB0.0710.0020.074
mergeBatches0.2190.0030.228
mergeExp0.0000.0000.001
modelPrior0.5870.0040.607
modelPriorAS-class0.0010.0000.001
pathCounts-class0.0000.0000.001
pathCounts0.0000.0000.001
plot-methods000
plotExpr000
plotPriorAS000
probNonEquiv0.1710.0010.179
procBam-class0.0010.0000.001
procBam000
procGenome0.0010.0000.001
qqnormGenomeWide0.0540.0010.057
quantileNorm0.0180.0010.018
relexprByGene0.0010.0000.000
rmShortInserts0.0010.0000.000
simMAE0.0010.0000.001
simMAEcheck0.0010.0000.001
simMultSamples0.0010.0000.000
simReads0.4000.0070.420
simulatedSamples-class0.0010.0000.001
splitGenomeByLength0.0000.0000.001
transcripts0.1830.0030.203
wrapDenovo0.0010.0010.000
wrapKnown0.0010.0000.001