Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:33:05 -0400 (Wed, 17 Oct 2018).
Package 1076/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
pdInfoBuilder 1.44.0 Benilton Carvalho
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: pdInfoBuilder |
Version: 1.44.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pdInfoBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.44.0.tar.gz |
StartedAt: 2018-10-17 03:54:39 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 03:58:30 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 231.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pdInfoBuilder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pdInfoBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/pdInfoBuilder.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 'pdInfoBuilder/DESCRIPTION' ... OK * this is package 'pdInfoBuilder' version '1.44.0' * 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 whether package 'pdInfoBuilder' 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 * 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 ... NOTE Namespaces in Imports field not imported from: 'BiocGenerics' 'IRanges' 'oligoClasses' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE cdf2table: no visible global function definition for 'getDoParWorkers' cdf2table: no visible global function definition for '%dopar%' cdf2table: no visible global function definition for 'foreach' cdf2table: no visible binding for global variable 'unitLst' cdfUnits2table: no visible global function definition for '%do%' cdfUnits2table: no visible global function definition for 'foreach' cdfUnits2table: no visible binding for global variable 'i' connectDb: no visible global function definition for 'dbGetQuery' createChrDict: no visible global function definition for 'na.omit' createIndicesDb : makeIndex: no visible global function definition for 'dbGetQuery' createIndicesDb: no visible global function definition for 'dbGetQuery' createSeqMat: no visible global function definition for 'dbGetQuery' createSeqMat.cnv: no visible global function definition for 'dbGetQuery' createTableInfoTable: no visible global function definition for 'dbGetQuery' dbCreateIndex: no visible global function definition for 'dbGetQuery' dbCreateTable: no visible global function definition for 'dbGetQuery' dbCreateTableInfo: no visible global function definition for 'dbGetQuery' getAllFSetMpsTables: no visible global function definition for '%dopar%' getAllFSetMpsTables: no visible global function definition for 'foreach' getAllFSetMpsTables: no visible binding for global variable 'i' increaseDbPerformance: no visible global function definition for 'dbGetQuery' initDb: no visible global function definition for 'dbGetQuery' insertInFragmentLengthTable: no visible global function definition for 'dbGetQuery' loadAffySeqCsv: no visible global function definition for 'dbGetQuery' loadUnits: no visible global function definition for 'dbGetQuery' parseBpmapCel: no visible global function definition for 'aggregate' parseCdfSeqAnnotSnp: no visible global function definition for 'aggregate' parseNgsTrio: no visible global function definition for 'aggregate' snp6.createIndicesDb : makeIndex: no visible global function definition for 'dbGetQuery' snp6.createIndicesDb: no visible global function definition for 'dbGetQuery' snp6.createTableInfoTable: no visible global function definition for 'dbGetQuery' snp6.initDb: no visible global function definition for 'dbGetQuery' snp6.loadUnits.cnv: no visible global function definition for 'dbGetQuery' snp6.loadUnits.snp: no visible global function definition for 'dbGetQuery' snp6.sortFeatureTables: no visible global function definition for 'dbGetQuery' sortFeatureTables: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffyClariomSPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffyExpressionPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffyHTAPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffyMiRNAPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffySNPCNVPDInfoPkgSeed2: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffySNPPDInfoPkgSeed2: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffySTPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,AffyTilingPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,GenericPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,NgsExpressionPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' makePdInfoPackage,NgsTilingPDInfoPkgSeed: no visible global function definition for 'dbGetQuery' Undefined global functions or variables: %do% %dopar% aggregate dbGetQuery foreach getDoParWorkers i na.omit unitLst Consider adding importFrom("stats", "aggregate", "na.omit") 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/pdInfoBuilder/libs/i386/pdInfoBuilder.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/pdInfoBuilder.Rcheck/00check.log' for details.
pdInfoBuilder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/pdInfoBuilder_1.44.0.tar.gz && rm -rf pdInfoBuilder.buildbin-libdir && mkdir pdInfoBuilder.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pdInfoBuilder.buildbin-libdir pdInfoBuilder_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL pdInfoBuilder_1.44.0.zip && rm pdInfoBuilder_1.44.0.tar.gz pdInfoBuilder_1.44.0.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 359k 100 359k 0 0 6169k 0 --:--:-- --:--:-- --:--:-- 6917k install for i386 * installing *source* package 'pdInfoBuilder' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c pdInfoBuilder.c -o pdInfoBuilder.o C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o pdInfoBuilder.dll tmp.def pdInfoBuilder.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'pdInfoBuilder' ** help *** installing help indices converting help for package 'pdInfoBuilder' finding HTML links ... done AffyClariomSPDInfoPkgSeed-class html AffyExpressionPDInfoPkgSeed-class html AffySNPCNVPDInfoPkgSeed-class html AffySNPCNVPDInfoPkgSeed2-class html AffySNPPDInfoPkgSeed-class html AffySNPPDInfoPkgSeed2-class html AffySTPDInfoPkgSeed-class html AffyTilingPDInfoPkgSeed-class html GenericArrayFunctions html NgsExpressionPDInfoPkgSeed-class html NgsTilingPDInfoPkgSeed-class html NimbleGenPDInfoPkgSeed-class html chipName html getGeometry html makePdInfoPackage html ** building package indices ** installing vignettes 'BuildingPDInfoPkgs.Rnw' 'howto-AffymetrixMapping.Rnw' ** testing if installed package can be loaded No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'pdInfoBuilder' In R CMD INSTALL install for x64 * installing *source* package 'pdInfoBuilder' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c pdInfoBuilder.c -o pdInfoBuilder.o C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o pdInfoBuilder.dll tmp.def pdInfoBuilder.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x64 ** testing if installed package can be loaded No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'pdInfoBuilder' * MD5 sums packaged installation of 'pdInfoBuilder' as pdInfoBuilder_1.44.0.zip * DONE (pdInfoBuilder) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'pdInfoBuilder' successfully unpacked and MD5 sums checked In R CMD INSTALL
pdInfoBuilder.Rcheck/examples_i386/pdInfoBuilder-Ex.timings
|
pdInfoBuilder.Rcheck/examples_x64/pdInfoBuilder-Ex.timings
|