David Rossell
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/casper |
| Branch: master |
| Last Commit: fd2e59a |
| Last Changed Date: 2019-01-04 13:21:12 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:27:50 -0400 (Tue, 09 Apr 2019).
| Package 210/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| casper 2.17.1 David Rossell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
| Package: casper |
| Version: 2.17.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:casper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings casper_2.17.1.tar.gz |
| StartedAt: 2019-04-08 23:40:48 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:46:26 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 337.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: casper.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:casper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings casper_2.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * 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 ‘2.17.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘casper’ can be installed ... WARNING Found the following significant warnings: seppel.cpp:484:2: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete] Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item' Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:58: unknown macro '\item' See ‘/Users/biocbuild/bbs-3.9-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 ... 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 ... WARNING prepare_Rd: man/getDistrs.Rd:47: unknown macro '\item' prepare_Rd: man/getDistrs.Rd:54: unknown macro '\item' prepare_Rd: man/getDistrs.Rd:58: unknown macro '\item' * 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 * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck/00check.log’ for details.
casper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL casper
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘casper’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c casper.cpp -o casper.o
clang++ -std=gnu++11 -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c dataframe.cpp -o dataframe.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c discretedf.cpp -o discretedf.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c dropVariant.cpp -o dropVariant.o
clang++ -std=gnu++11 -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++ -std=gnu++11 -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c model.cpp -o model.o
clang++ -std=gnu++11 -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rcasper.cpp -o rcasper.o
clang++ -std=gnu++11 -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++ -std=gnu++11 -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c variant.cpp -o variant.o
clang++ -std=gnu++11 -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++ -std=gnu++11 -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/casper/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘transcripts’ in package ‘casper’
** help
Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:58: unknown macro '\item'
*** installing help indices
** building package indices
** installing vignettes
‘casper.Rnw’
** testing if installed package can be loaded
* DONE (casper)
casper.Rcheck/casper-Ex.timings
| name | user | system | elapsed | |
| K562.r1l1 | 0.248 | 0.010 | 0.261 | |
| annotatedGenome-class | 0.001 | 0.000 | 0.002 | |
| asymmetryCheck | 0.037 | 0.001 | 0.039 | |
| calcDenovo | 0 | 0 | 0 | |
| calcExp | 3.273 | 0.483 | 3.796 | |
| denovoExpr | 4.224 | 0.543 | 4.808 | |
| denovoGeneExpr-class | 0.001 | 0.000 | 0.002 | |
| denovoGenomeExpr-class | 0.000 | 0.000 | 0.001 | |
| distrsGSE37704 | 0.201 | 0.013 | 0.222 | |
| genePlot | 0.324 | 0.031 | 0.360 | |
| getDistrs | 0.488 | 0.022 | 0.515 | |
| getIsland | 0.109 | 0.005 | 0.116 | |
| getNreads | 0 | 0 | 0 | |
| getReads | 0 | 0 | 0 | |
| getRoc | 0 | 0 | 0 | |
| hg19DB | 0.107 | 0.010 | 0.118 | |
| mergeBatches | 0.102 | 0.002 | 0.105 | |
| mergeExp | 0.000 | 0.000 | 0.001 | |
| modelPrior | 0.493 | 0.018 | 0.520 | |
| modelPriorAS-class | 0.001 | 0.000 | 0.000 | |
| pathCounts-class | 0.001 | 0.000 | 0.001 | |
| pathCounts | 0 | 0 | 0 | |
| plot-methods | 0.000 | 0.000 | 0.001 | |
| plotExpr | 0 | 0 | 0 | |
| plotPriorAS | 0.000 | 0.000 | 0.001 | |
| probNonEquiv | 0.126 | 0.004 | 0.135 | |
| procBam-class | 0.001 | 0.001 | 0.001 | |
| procBam | 0 | 0 | 0 | |
| procGenome | 0.000 | 0.001 | 0.001 | |
| qqnormGenomeWide | 0.087 | 0.003 | 0.094 | |
| quantileNorm | 0.013 | 0.002 | 0.015 | |
| relexprByGene | 0.000 | 0.000 | 0.001 | |
| rmShortInserts | 0.001 | 0.001 | 0.000 | |
| simMAE | 0.001 | 0.000 | 0.000 | |
| simMAEcheck | 0 | 0 | 0 | |
| simMultSamples | 0 | 0 | 0 | |
| simReads | 0.454 | 0.018 | 0.478 | |
| simulatedSamples-class | 0.001 | 0.000 | 0.002 | |
| splitGenomeByLength | 0.000 | 0.001 | 0.000 | |
| transcripts | 0.169 | 0.006 | 0.177 | |
| wrapDenovo | 0.001 | 0.000 | 0.000 | |
| wrapKnown | 0.000 | 0.001 | 0.001 | |