Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:55:21 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE pdInfoBuilder PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1288/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
pdInfoBuilder 1.52.0 Benilton Carvalho
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: pdInfoBuilder |
Version: 1.52.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:pdInfoBuilder.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings pdInfoBuilder_1.52.0.tar.gz |
StartedAt: 2020-10-17 04:00:20 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 04:03:24 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 184.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pdInfoBuilder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:pdInfoBuilder.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings pdInfoBuilder_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/pdInfoBuilder.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pdInfoBuilder/DESCRIPTION’ ... OK * this is package ‘pdInfoBuilder’ version ‘1.52.0’ * 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 ‘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 * 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 is not available * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 ‘/home/biocbuild/bbs-3.11-bioc/meat/pdInfoBuilder.Rcheck/00check.log’ for details.
pdInfoBuilder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL pdInfoBuilder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘pdInfoBuilder’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-pdInfoBuilder/00new/pdInfoBuilder/libs ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’ No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘pdInfoBuilder’ ** help *** installing help indices ** building package indices ** installing vignettes ‘BuildingPDInfoPkgs.Rnw’ ‘howto-AffymetrixMapping.Rnw’ ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’ No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘pdInfoBuilder’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’ No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘pdInfoBuilder’ ** testing if installed package keeps a record of temporary installation path * DONE (pdInfoBuilder)
pdInfoBuilder.Rcheck/pdInfoBuilder-Ex.timings
name | user | system | elapsed | |
AffyClariomSPDInfoPkgSeed-class | 0.003 | 0.000 | 0.003 | |
AffyExpressionPDInfoPkgSeed-class | 0.001 | 0.000 | 0.001 | |
AffySNPCNVPDInfoPkgSeed-class | 0.002 | 0.000 | 0.002 | |
AffySNPCNVPDInfoPkgSeed2-class | 0.001 | 0.000 | 0.001 | |
AffySNPPDInfoPkgSeed-class | 0.505 | 0.004 | 0.508 | |
AffySNPPDInfoPkgSeed2-class | 0.001 | 0.000 | 0.001 | |
AffySTPDInfoPkgSeed-class | 0.000 | 0.001 | 0.002 | |
AffyTilingPDInfoPkgSeed-class | 0.000 | 0.002 | 0.001 | |
NgsExpressionPDInfoPkgSeed-class | 0.000 | 0.001 | 0.001 | |
NgsTilingPDInfoPkgSeed-class | 0.001 | 0.000 | 0.002 | |
NimbleGenPDInfoPkgSeed-class | 0.001 | 0.000 | 0.001 | |
makePdInfoPackage | 0 | 0 | 0 | |