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This page was generated on 2024-04-17 11:37:06 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1518/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pdInfoBuilder 1.66.0  (landing page)
Benilton Carvalho
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/pdInfoBuilder
git_branch: RELEASE_3_18
git_last_commit: 7e41f73
git_last_commit_date: 2023-10-24 09:37:47 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for pdInfoBuilder on palomino4


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.

raw results


Summary

Package: pdInfoBuilder
Version: 1.66.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pdInfoBuilder.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.66.0.tar.gz
StartedAt: 2024-04-16 03:39:11 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 03:42:36 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 204.8 seconds
RetCode: 0
Status:   OK  
CheckDir: pdInfoBuilder.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pdInfoBuilder.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* 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 '1.66.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* 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 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 x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/pdInfoBuilder/libs/x64/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 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 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
  'F:/biocbuild/bbs-3.18-bioc/meat/pdInfoBuilder.Rcheck/00check.log'
for details.



Installation output

pdInfoBuilder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL pdInfoBuilder
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'pdInfoBuilder' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-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)

Tests output


Example timings

pdInfoBuilder.Rcheck/pdInfoBuilder-Ex.timings

nameusersystemelapsed
AffyClariomSPDInfoPkgSeed-class000
AffyExpressionPDInfoPkgSeed-class000
AffySNPCNVPDInfoPkgSeed-class000
AffySNPCNVPDInfoPkgSeed2-class0.010.000.01
AffySNPPDInfoPkgSeed-class0.470.020.49
AffySNPPDInfoPkgSeed2-class000
AffySTPDInfoPkgSeed-class000
AffyTilingPDInfoPkgSeed-class000
NgsExpressionPDInfoPkgSeed-class000
NgsTilingPDInfoPkgSeed-class000
NimbleGenPDInfoPkgSeed-class000
makePdInfoPackage000