Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:44:30 -0400 (Wed, 17 Oct 2018).
Package 743/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
InterMineR 1.2.1 InterMine Team
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
Package: InterMineR |
Version: 1.2.1 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterMineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings InterMineR_1.2.1.tar.gz |
StartedAt: 2018-10-17 02:48:41 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 02:55:46 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 424.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: InterMineR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterMineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings InterMineR_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/InterMineR.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'InterMineR/DESCRIPTION' ... OK * this is package 'InterMineR' version '1.2.1' * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'InterMineR' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:5: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:8: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:38: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:56: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:59: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:66: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGeneAnswers.Rd:8: file link 'GeneAnswers' in package 'GeneAnswers' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:5: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:8: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:43: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:46: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:52: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:54: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:58: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:61: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:69: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/InterMineR.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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 * 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 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 convertToGeneAnswers: no visible binding for global variable 'geneExpProfile' convertToRangedSummarizedExperiment: no visible global function definition for 'reshape' doEnrichment: no visible global function definition for 'URLencode' listDatasets: no visible binding for global variable 'child_name' runQuery,ANY-InterMineR: no visible global function definition for 'URLencode' runQuery,ANY-list: no visible global function definition for 'URLencode' Undefined global functions or variables: URLencode child_name geneExpProfile reshape Consider adding importFrom("stats", "reshape") importFrom("utils", "URLencode") to your NAMESPACE file. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed convertToGeneAnswers 16.54 0.38 25.05 simplifyResult 6.89 0.08 8.17 doEnrichment 5.42 0.19 37.55 convertToRangedSummarizedExperiment 3.33 0.01 6.83 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed convertToGeneAnswers 19.97 0.25 28.26 simplifyResult 12.39 0.03 13.84 doEnrichment 6.24 0.19 38.77 runQuery 4.94 0.06 6.53 convertToRangedSummarizedExperiment 4.41 0.01 7.95 listDatasets 4.17 0.02 6.14 * 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 'C:/Users/biocbuild/bbs-3.7-bioc/meat/InterMineR.Rcheck/00check.log' for details.
InterMineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/InterMineR_1.2.1.tar.gz && rm -rf InterMineR.buildbin-libdir && mkdir InterMineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InterMineR.buildbin-libdir InterMineR_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL InterMineR_1.2.1.zip && rm InterMineR_1.2.1.tar.gz InterMineR_1.2.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1741k 100 1741k 0 0 24.9M 0 --:--:-- --:--:-- --:--:-- 27.4M install for i386 * installing *source* package 'InterMineR' ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'InterMineR' finding HTML links ... done InterMineR-class html InterMineR-methods html InterMineR-package html PL_DiabetesGenes html PL_FlyTF_site_specific_TFs html convertToGRanges html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:5: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:8: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:38: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:56: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:59: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGRanges.Rd:66: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic convertToGeneAnswers html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToGeneAnswers.Rd:8: file link 'GeneAnswers' in package 'GeneAnswers' does not exist and so has been treated as a topic convertToRangedSummarizedExperiment html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:5: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:8: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:43: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:46: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:52: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:54: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:58: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:61: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2JFtDb/R.INSTALLec4ec33786/InterMineR/man/convertToRangedSummarizedExperiment.Rd:69: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic doEnrichment html getDatasets html getGeneIds html getModel html getRelease html getTemplateQuery html getTemplates html getVersion html getWidgets html initInterMine html listDatasets html listMines html newQuery html runQuery html setConstraints html setQuery html simplifyResult html summary html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'InterMineR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'InterMineR' as InterMineR_1.2.1.zip * DONE (InterMineR) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'InterMineR' successfully unpacked and MD5 sums checked In R CMD INSTALL
InterMineR.Rcheck/examples_i386/InterMineR-Ex.timings
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InterMineR.Rcheck/examples_x64/InterMineR-Ex.timings
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