David Rossell
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/casper |
| Branch: RELEASE_3_6 |
| Last Commit: b391807 |
| Last Changed Date: 2017-10-30 12:39:59 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:10:53 -0400 (Thu, 12 Apr 2018).
| Package 182/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| casper 2.12.0 David Rossell
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: casper |
| Version: 2.12.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings casper_2.12.0.tar.gz |
| StartedAt: 2018-04-11 22:01:49 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:05:53 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 244.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: casper.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings casper_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.12.0’
* 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:
Warning: /home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00_pkg_src/casper/man/getDistrs.Rd:47: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00_pkg_src/casper/man/getDistrs.Rd:54: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00_pkg_src/casper/man/getDistrs.Rd:58: unknown macro '\item'
See ‘/home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 1.8Mb
libs 2.8Mb
* 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 ... WARNING
prepare_Rd: getDistrs.Rd:47: unknown macro '\item'
prepare_Rd: getDistrs.Rd:54: unknown macro '\item'
prepare_Rd: 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 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 5.22 0.168 5.393
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00check.log’
for details.
casper.Rcheck/00install.out
* installing *source* package ‘casper’ ... ** libs g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c casper.cpp -o casper.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cstat.cpp -o cstat.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dataframe.cpp -o dataframe.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c discretedf.cpp -o discretedf.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dropVariant.cpp -o dropVariant.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exon.cpp -o exon.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fragFunc.c -o fragFunc.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fragment.cpp -o fragment.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c functions.c -o functions.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash.c -o hash.o gcc -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c makeIslands.c -o makeIslands.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c model.cpp -o model.o g++ -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pathCounts.c -o pathCounts.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c procBam.c -o procBam.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rcasper.cpp -o rcasper.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c seppel.cpp -o seppel.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c simReads.c -o simReads.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c simReadsfunc.c -o simReadsfunc.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c smartmodeldist.cpp -o smartmodeldist.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uniqQname.c -o uniqQname.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c variant.cpp -o variant.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c variant_cmp.cpp -o variant_cmp.o g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-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 Warning: /home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00_pkg_src/casper/man/getDistrs.Rd:47: unknown macro '\item' Warning: /home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00_pkg_src/casper/man/getDistrs.Rd:54: unknown macro '\item' Warning: /home/biocbuild/bbs-3.6-bioc/meat/casper.Rcheck/00_pkg_src/casper/man/getDistrs.Rd:58: unknown macro '\item' *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (casper)
casper.Rcheck/casper-Ex.timings
| name | user | system | elapsed | |
| K562.r1l1 | 0.160 | 0.036 | 0.198 | |
| annotatedGenome-class | 0.000 | 0.000 | 0.001 | |
| asymmetryCheck | 0.112 | 0.000 | 0.110 | |
| calcDenovo | 0 | 0 | 0 | |
| calcExp | 3.168 | 0.168 | 3.337 | |
| denovoExpr | 5.220 | 0.168 | 5.393 | |
| denovoGeneExpr-class | 0.004 | 0.000 | 0.001 | |
| denovoGenomeExpr-class | 0 | 0 | 0 | |
| distrsGSE37704 | 0.156 | 0.004 | 0.161 | |
| genePlot | 0.448 | 0.000 | 0.449 | |
| getDistrs | 0.372 | 0.028 | 0.402 | |
| getIsland | 0.084 | 0.004 | 0.085 | |
| getNreads | 0 | 0 | 0 | |
| getReads | 0 | 0 | 0 | |
| getRoc | 0 | 0 | 0 | |
| hg19DB | 0.080 | 0.000 | 0.082 | |
| mergeBatches | 0.2 | 0.0 | 0.2 | |
| mergeExp | 0 | 0 | 0 | |
| modelPrior | 0.564 | 0.000 | 0.586 | |
| modelPriorAS-class | 0.000 | 0.000 | 0.001 | |
| pathCounts-class | 0.000 | 0.000 | 0.001 | |
| pathCounts | 0.000 | 0.000 | 0.001 | |
| plot-methods | 0 | 0 | 0 | |
| plotExpr | 0.000 | 0.000 | 0.001 | |
| plotPriorAS | 0 | 0 | 0 | |
| probNonEquiv | 0.204 | 0.000 | 0.205 | |
| procBam-class | 0.004 | 0.000 | 0.001 | |
| procBam | 0 | 0 | 0 | |
| procGenome | 0.000 | 0.000 | 0.001 | |
| qqnormGenomeWide | 0.060 | 0.000 | 0.061 | |
| quantileNorm | 0.02 | 0.00 | 0.02 | |
| relexprByGene | 0 | 0 | 0 | |
| rmShortInserts | 0.004 | 0.000 | 0.000 | |
| simMAE | 0.000 | 0.000 | 0.001 | |
| simMAEcheck | 0.000 | 0.000 | 0.001 | |
| simMultSamples | 0.000 | 0.000 | 0.001 | |
| simReads | 0.376 | 0.028 | 0.408 | |
| simulatedSamples-class | 0.000 | 0.000 | 0.001 | |
| splitGenomeByLength | 0 | 0 | 0 | |
| transcripts | 0.164 | 0.000 | 0.164 | |
| wrapDenovo | 0.000 | 0.000 | 0.001 | |
| wrapKnown | 0.000 | 0.000 | 0.001 | |