Kieran O'Neill
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/contiBAIT |
| Branch: RELEASE_3_10 |
| Last Commit: 362c9cb |
| Last Changed Date: 2019-10-29 13:09:34 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:10:58 -0400 (Wed, 15 Apr 2020).
| Package 356/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| contiBAIT 1.14.0 Kieran O'Neill
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: contiBAIT |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings contiBAIT_1.14.0.tar.gz |
| StartedAt: 2020-04-15 03:33:54 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:39:41 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 347.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: contiBAIT.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings contiBAIT_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/contiBAIT.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘contiBAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘contiBAIT’ version ‘1.14.0’
* 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 ‘contiBAIT’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
extdata 3.4Mb
libs 1.2Mb
* 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
ideogramPlot.func: no visible binding for global variable ‘w’
ideogramPlot.func: no visible binding for global variable ‘w2’
makeChrTable: no visible global function definition for ‘queryHits’
makeChrTable: no visible global function definition for ‘subjectHits’
orderContigsGreedy: no visible global function definition for
‘makeCluster’
orderContigsGreedy: no visible global function definition for
‘clusterCall’
orderContigsGreedy: no visible global function definition for
‘stopCluster’
strandSeqFreqTable: no visible global function definition for
‘queryHits’
strandSeqFreqTable: no visible global function definition for
‘subjectHits’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
binding for global variable ‘w’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
binding for global variable ‘w2’
Undefined global functions or variables:
clusterCall makeCluster queryHits stopCluster subjectHits w w2
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotLGDistances,LinkageGroupList,StrandStateMatrix-method':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
contiBAIT 7.264 0.360 8.832
findSimilarLibraries 4.800 0.976 5.954
* 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.
contiBAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL contiBAIT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘contiBAIT’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c buildLinkageGroups.cpp -o buildLinkageGroups.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c computeSim.cpp -o computeSim.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c orderContigsGreedy.cpp -o orderContigsGreedy.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-contiBAIT/00new/contiBAIT/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (contiBAIT)
contiBAIT.Rcheck/contiBAIT-Ex.timings
| name | user | system | elapsed | |
| BAIT | 0 | 0 | 0 | |
| ContigOrdering | 0.000 | 0.000 | 0.002 | |
| LibraryGroupList | 0.016 | 0.000 | 0.015 | |
| LinkageGroupList | 0.000 | 0.000 | 0.001 | |
| StrandFreqMatrix | 0.072 | 0.000 | 0.072 | |
| StrandReadMatrix | 0.020 | 0.000 | 0.019 | |
| StrandStateMatrix | 0.004 | 0.000 | 0.003 | |
| barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method | 0.636 | 0.004 | 0.641 | |
| clusterContigs-StrandStateMatrix-method | 0.028 | 0.000 | 0.031 | |
| contiBAIT | 7.264 | 0.360 | 8.832 | |
| findSimilarLibraries | 4.800 | 0.976 | 5.954 | |
| ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method | 3.332 | 0.056 | 3.683 | |
| makeBoxPlot | 0.036 | 0.000 | 0.038 | |
| makeChrTable | 1.476 | 0.000 | 1.527 | |
| orderAllLinkageGroups | 1.728 | 0.012 | 1.788 | |
| plotContigOrder | 0.448 | 0.012 | 0.461 | |
| plotLGDistances-LinkageGroupList-StrandStateMatrix-method | 0.168 | 0.004 | 0.169 | |
| plotWCdistribution-StrandFreqMatrix-method | 0.084 | 0.008 | 0.093 | |
| preprocessStrandTable-StrandFreqMatrix-method | 0.280 | 0.000 | 0.278 | |
| reorientAndMergeLGs | 0.144 | 0.004 | 0.148 | |
| strandSeqFreqTable | 4.636 | 0.028 | 4.689 | |
| thoroughBed | 0.048 | 0.000 | 0.049 | |
| writeBed | 0 | 0 | 0 | |