Nuno Saraiva-Agostinho
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_5 |
| Last Commit: 9caf5da |
| Last Changed Date: 2017-04-25 18:33:25 -0400 (Tue, 25 Apr 2017) |
| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O [P] Q R S T U V W X Y Z |
This page was generated on 2017-10-18 14:26:35 -0400 (Wed, 18 Oct 2017).
| Package 1025/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psichomics 1.2.1 Nuno Saraiva-Agostinho
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: psichomics |
| Version: 1.2.1 |
| Command: rm -rf psichomics.buildbin-libdir psichomics.Rcheck && mkdir psichomics.buildbin-libdir psichomics.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psichomics.buildbin-libdir psichomics_1.2.1.tar.gz >psichomics.Rcheck\00install.out 2>&1 && cp psichomics.Rcheck\00install.out psichomics-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=psichomics.buildbin-libdir --install="check:psichomics-install.out" --force-multiarch --no-vignettes --timings psichomics_1.2.1.tar.gz |
| StartedAt: 2017-10-18 02:11:50 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 02:17:59 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 368.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: psichomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf psichomics.buildbin-libdir psichomics.Rcheck && mkdir psichomics.buildbin-libdir psichomics.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=psichomics.buildbin-libdir psichomics_1.2.1.tar.gz >psichomics.Rcheck\00install.out 2>&1 && cp psichomics.Rcheck\00install.out psichomics-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=psichomics.buildbin-libdir --install="check:psichomics-install.out" --force-multiarch --no-vignettes --timings psichomics_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/psichomics.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'psichomics/DESCRIPTION' ... OK
* this is package 'psichomics' version '1.2.1'
* package encoding: UTF-8
* 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 'psichomics' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
hchart.survfit 1.13 0.08 10.10
plotVariance 0.08 0.07 6.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotPCA 0.39 0.16 8.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: OK
psichomics.Rcheck/00install.out:
install for i386 * installing *source* package 'psichomics' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'psichomics' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'psichomics' as psichomics_1.2.1.zip * DONE (psichomics)
psichomics.Rcheck/examples_i386/psichomics-Ex.timings:
| name | user | system | elapsed | |
| createGroupByAttribute | 0 | 0 | 0 | |
| createJunctionsTemplate | 0 | 0 | 0 | |
| diffAnalyses | 0.62 | 0.06 | 0.68 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.27 | 0.03 | 0.57 | |
| filterGroups | 0 | 0 | 0 | |
| getDownloadsFolder | 0 | 0 | 0 | |
| getFirebrowseCohorts | 0.23 | 0.00 | 0.31 | |
| getFirebrowseDataTypes | 0.03 | 0.00 | 0.03 | |
| getFirebrowseDateFormat | 0 | 0 | 0 | |
| getFirebrowseDates | 0.01 | 0.00 | 0.04 | |
| getMatchingSamples | 0 | 0 | 0 | |
| getNumerics | 0 | 0 | 0 | |
| getPatientFromSample | 0 | 0 | 0 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getValidEvents | 0.01 | 0.00 | 0.01 | |
| groupPerPatient | 0 | 0 | 0 | |
| groupPerSample | 0 | 0 | 0 | |
| hchart.survfit | 1.13 | 0.08 | 10.10 | |
| isFirebrowseUp | 0.03 | 0.00 | 0.06 | |
| labelBasedOnCutoff | 0.02 | 0.00 | 0.02 | |
| leveneTest | 0.01 | 0.00 | 0.01 | |
| listAllAnnotations | 0 | 0 | 0 | |
| listSplicingAnnotations | 0 | 0 | 0 | |
| loadAnnotation | 0 | 0 | 0 | |
| loadFirebrowseData | 0 | 0 | 0 | |
| loadLocalFiles | 0 | 0 | 0 | |
| missingDataModal | 0 | 0 | 0 | |
| optimalPSIcutoff | 0.28 | 0.00 | 0.28 | |
| parseFirebrowseMetadata | 0.03 | 0.01 | 0.17 | |
| parseMatsEvent | 0.02 | 0.00 | 0.02 | |
| parseMatsGeneric | 0.06 | 0.00 | 0.06 | |
| parseMisoAnnotation | 0.67 | 0.00 | 0.67 | |
| parseMisoEvent | 0.02 | 0.00 | 0.02 | |
| parseMisoEventID | 0 | 0 | 0 | |
| parseMisoGeneric | 0.14 | 0.02 | 0.16 | |
| parseMisoId | 0 | 0 | 0 | |
| parseSampleGroups | 0 | 0 | 0 | |
| parseSplicingEvent | 0 | 0 | 0 | |
| parseSuppaEvent | 0.02 | 0.00 | 0.01 | |
| parseSuppaGeneric | 0.01 | 0.00 | 0.02 | |
| parseUrlsFromFirebrowseResponse | 0.01 | 0.00 | 0.09 | |
| parseVastToolsEvent | 0.02 | 0.00 | 0.01 | |
| parseVastToolsSE | 0.14 | 0.00 | 0.15 | |
| performPCA | 0 | 0 | 0 | |
| plotDistribution | 0.57 | 0.02 | 0.61 | |
| plotPCA | 0.32 | 0.09 | 0.41 | |
| plotProtein | 0 | 0 | 0 | |
| plotSurvivalCurves | 0.16 | 0.05 | 0.21 | |
| plotTranscripts | 0.01 | 0.00 | 1.07 | |
| plotVariance | 0.08 | 0.07 | 6.18 | |
| prepareAnnotationFromEvents | 0.42 | 0.02 | 0.43 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| processSurvTerms | 0.02 | 0.00 | 0.02 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.03 | 0.00 | 0.03 | |
| queryEnsembl | 0.03 | 0.00 | 0.58 | |
| queryEnsemblByEvent | 0.08 | 0.00 | 1.44 | |
| queryEnsemblByGene | 0.14 | 0.00 | 1.83 | |
| queryFirebrowseData | 0.15 | 0.00 | 0.28 | |
| queryPubMed | 0.08 | 0.00 | 0.28 | |
| queryUniprot | 0.13 | 0.02 | 1.80 | |
| readFile | 0 | 0 | 0 | |
| renameDuplicated | 0 | 0 | 0 | |
| survdiff.survTerms | 0.01 | 0.00 | 0.01 | |
| survfit.survTerms | 0.03 | 0.00 | 0.04 | |
| testSurvival | 0.03 | 0.00 | 0.03 | |
| textSuggestions | 0 | 0 | 0 | |
| trimWhitespace | 0 | 0 | 0 | |
psichomics.Rcheck/examples_x64/psichomics-Ex.timings:
| name | user | system | elapsed | |
| createGroupByAttribute | 0 | 0 | 0 | |
| createJunctionsTemplate | 0 | 0 | 0 | |
| diffAnalyses | 0.53 | 0.00 | 0.53 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.61 | 0.05 | 0.89 | |
| filterGroups | 0 | 0 | 0 | |
| getDownloadsFolder | 0 | 0 | 0 | |
| getFirebrowseCohorts | 0.20 | 0.02 | 0.28 | |
| getFirebrowseDataTypes | 0.05 | 0.00 | 0.05 | |
| getFirebrowseDateFormat | 0 | 0 | 0 | |
| getFirebrowseDates | 0.00 | 0.00 | 0.06 | |
| getMatchingSamples | 0 | 0 | 0 | |
| getNumerics | 0.01 | 0.00 | 0.02 | |
| getPatientFromSample | 0 | 0 | 0 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getValidEvents | 0 | 0 | 0 | |
| groupPerPatient | 0 | 0 | 0 | |
| groupPerSample | 0 | 0 | 0 | |
| hchart.survfit | 1.21 | 0.12 | 3.89 | |
| isFirebrowseUp | 0.02 | 0.00 | 0.03 | |
| labelBasedOnCutoff | 0.03 | 0.00 | 0.03 | |
| leveneTest | 0.02 | 0.00 | 0.02 | |
| listAllAnnotations | 0 | 0 | 0 | |
| listSplicingAnnotations | 0 | 0 | 0 | |
| loadAnnotation | 0 | 0 | 0 | |
| loadFirebrowseData | 0 | 0 | 0 | |
| loadLocalFiles | 0 | 0 | 0 | |
| missingDataModal | 0 | 0 | 0 | |
| optimalPSIcutoff | 0.31 | 0.00 | 0.32 | |
| parseFirebrowseMetadata | 0.06 | 0.00 | 0.17 | |
| parseMatsEvent | 0.02 | 0.00 | 0.01 | |
| parseMatsGeneric | 0.03 | 0.00 | 0.04 | |
| parseMisoAnnotation | 0.61 | 0.00 | 0.60 | |
| parseMisoEvent | 0.01 | 0.00 | 0.02 | |
| parseMisoEventID | 0 | 0 | 0 | |
| parseMisoGeneric | 0.13 | 0.00 | 0.12 | |
| parseMisoId | 0 | 0 | 0 | |
| parseSampleGroups | 0 | 0 | 0 | |
| parseSplicingEvent | 0 | 0 | 0 | |
| parseSuppaEvent | 0 | 0 | 0 | |
| parseSuppaGeneric | 0.04 | 0.00 | 0.03 | |
| parseUrlsFromFirebrowseResponse | 0.01 | 0.00 | 0.11 | |
| parseVastToolsEvent | 0.02 | 0.00 | 0.01 | |
| parseVastToolsSE | 0.18 | 0.00 | 0.19 | |
| performPCA | 0 | 0 | 0 | |
| plotDistribution | 0.55 | 0.05 | 0.59 | |
| plotPCA | 0.39 | 0.16 | 8.64 | |
| plotProtein | 0 | 0 | 0 | |
| plotSurvivalCurves | 0.14 | 0.06 | 0.36 | |
| plotTranscripts | 0.04 | 0.00 | 0.91 | |
| plotVariance | 0.08 | 0.00 | 0.07 | |
| prepareAnnotationFromEvents | 0.38 | 0.00 | 0.38 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| processSurvTerms | 0 | 0 | 0 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.03 | 0.00 | 0.03 | |
| queryEnsembl | 0.05 | 0.00 | 0.56 | |
| queryEnsemblByEvent | 0.11 | 0.01 | 1.47 | |
| queryEnsemblByGene | 0.12 | 0.00 | 1.72 | |
| queryFirebrowseData | 0.14 | 0.00 | 0.30 | |
| queryPubMed | 0.06 | 0.02 | 0.29 | |
| queryUniprot | 0.1 | 0.0 | 1.6 | |
| readFile | 0 | 0 | 0 | |
| renameDuplicated | 0.01 | 0.00 | 0.01 | |
| survdiff.survTerms | 0.02 | 0.00 | 0.02 | |
| survfit.survTerms | 0.06 | 0.00 | 0.06 | |
| testSurvival | 0.03 | 0.01 | 0.05 | |
| textSuggestions | 0 | 0 | 0 | |
| trimWhitespace | 0 | 0 | 0 | |