Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 |
Package 1500/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pdInfoBuilder 1.69.3 (landing page) Benilton Carvalho
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: pdInfoBuilder |
Version: 1.69.3 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pdInfoBuilder.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.69.3.tar.gz |
StartedAt: 2024-08-21 03:41:03 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:44:42 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 219.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pdInfoBuilder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pdInfoBuilder.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.69.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/pdInfoBuilder.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'pdInfoBuilder/DESCRIPTION' ... OK * this is package 'pdInfoBuilder' version '1.69.3' * 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 * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 code 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 annot2fdata: no visible global function definition for 'error' 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 'dbExecute' 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 'dbExecute' dbCreateTable: no visible global function definition for 'dbExecute' 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 'dbExecute' 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 'dbExecute' 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 dbExecute dbGetQuery error 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 x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/pdInfoBuilder/libs/x64/pdInfoBuilder.dll': Found '_exit', possibly from '_exit' (C) 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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK * 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 ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/pdInfoBuilder.Rcheck/00check.log' for details.
pdInfoBuilder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL pdInfoBuilder ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'pdInfoBuilder' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pdInfoBuilder.c -o pdInfoBuilder.o gcc -shared -s -static-libgcc -o pdInfoBuilder.dll tmp.def pdInfoBuilder.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-pdInfoBuilder/00new/pdInfoBuilder/libs/x64 ** 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' ** 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 | 0.02 | 0.00 | 0.02 | |
AffyExpressionPDInfoPkgSeed-class | 0 | 0 | 0 | |
AffySNPCNVPDInfoPkgSeed-class | 0 | 0 | 0 | |
AffySNPCNVPDInfoPkgSeed2-class | 0 | 0 | 0 | |
AffySNPPDInfoPkgSeed-class | 0.32 | 0.02 | 0.33 | |
AffySNPPDInfoPkgSeed2-class | 0 | 0 | 0 | |
AffySTPDInfoPkgSeed-class | 0.00 | 0.01 | 0.02 | |
AffyTilingPDInfoPkgSeed-class | 0 | 0 | 0 | |
NgsExpressionPDInfoPkgSeed-class | 0 | 0 | 0 | |
NgsTilingPDInfoPkgSeed-class | 0 | 0 | 0 | |
NimbleGenPDInfoPkgSeed-class | 0 | 0 | 0 | |
makePdInfoPackage | 0 | 0 | 0 | |