Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:28 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the pdInfoBuilder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pdInfoBuilder.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1475/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pdInfoBuilder 1.63.0 (landing page) Benilton Carvalho
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: pdInfoBuilder |
Version: 1.63.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pdInfoBuilder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pdInfoBuilder_1.63.0.tar.gz |
StartedAt: 2023-04-11 22:20:28 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 22:26:45 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 377.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pdInfoBuilder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pdInfoBuilder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pdInfoBuilder_1.63.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pdInfoBuilder.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘pdInfoBuilder/DESCRIPTION’ ... OK * this is package ‘pdInfoBuilder’ version ‘1.63.0’ * 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 * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 loading without being on the library search path ... 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 ... ‘BuildingPDInfoPkgs.Rnw’... OK ‘howto-AffymetrixMapping.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/pdInfoBuilder.Rcheck/00check.log’ for details.
pdInfoBuilder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pdInfoBuilder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘pdInfoBuilder’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-pdInfoBuilder/00new/pdInfoBuilder/libs ** 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 ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location 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: ‘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 | 0.004 | 0.000 | 0.004 | |
AffyExpressionPDInfoPkgSeed-class | 0.001 | 0.000 | 0.002 | |
AffySNPCNVPDInfoPkgSeed-class | 0.002 | 0.000 | 0.002 | |
AffySNPCNVPDInfoPkgSeed2-class | 0.002 | 0.000 | 0.002 | |
AffySNPPDInfoPkgSeed-class | 0.501 | 0.271 | 0.773 | |
AffySNPPDInfoPkgSeed2-class | 0.002 | 0.000 | 0.003 | |
AffySTPDInfoPkgSeed-class | 0.000 | 0.002 | 0.002 | |
AffyTilingPDInfoPkgSeed-class | 0.002 | 0.000 | 0.002 | |
NgsExpressionPDInfoPkgSeed-class | 0.001 | 0.001 | 0.002 | |
NgsTilingPDInfoPkgSeed-class | 0.001 | 0.000 | 0.002 | |
NimbleGenPDInfoPkgSeed-class | 0.002 | 0.000 | 0.002 | |
makePdInfoPackage | 0.001 | 0.000 | 0.001 | |