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This page was generated on 2022-01-17 13:06:45 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for pdInfoBuilder on tokay2


To the developers/maintainers of the pdInfoBuilder package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1389/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pdInfoBuilder 1.58.0  (landing page)
Benilton Carvalho
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/pdInfoBuilder
git_branch: RELEASE_3_14
git_last_commit: 0988869
git_last_commit_date: 2021-10-26 11:50:45 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pdInfoBuilder
Version: 1.58.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pdInfoBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.58.0.tar.gz
StartedAt: 2022-01-17 01:17:57 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 01:21:40 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 222.9 seconds
RetCode: 0
Status:   OK  
CheckDir: pdInfoBuilder.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pdInfoBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.58.0'
* 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-3.14-bioc/R/library/pdInfoBuilder/libs/i386/pdInfoBuilder.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-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. 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-3.14-bioc/meat/pdInfoBuilder.Rcheck/00check.log'
for details.



Installation output

pdInfoBuilder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pdInfoBuilder_1.58.0.tar.gz && rm -rf pdInfoBuilder.buildbin-libdir && mkdir pdInfoBuilder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pdInfoBuilder.buildbin-libdir pdInfoBuilder_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pdInfoBuilder_1.58.0.zip && rm pdInfoBuilder_1.58.0.tar.gz pdInfoBuilder_1.58.0.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
 47  358k   47  170k    0     0  1074k      0 --:--:-- --:--:-- --:--:-- 1076k
100  358k  100  358k    0     0  1531k      0 --:--:-- --:--:-- --:--:-- 1533k

install for i386

* installing *source* package 'pdInfoBuilder' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pdInfoBuilder.c -o pdInfoBuilder.o
C:/rtools40/mingw32/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/pdInfoBuilder.buildbin-libdir/00LOCK-pdInfoBuilder/00new/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 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

install for x64

* installing *source* package 'pdInfoBuilder' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pdInfoBuilder.c -o pdInfoBuilder.o
C:/rtools40/mingw64/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-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_1.58.0.zip
* DONE (pdInfoBuilder)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'pdInfoBuilder' successfully unpacked and MD5 sums checked

Tests output


Example timings

pdInfoBuilder.Rcheck/examples_i386/pdInfoBuilder-Ex.timings

nameusersystemelapsed
AffyClariomSPDInfoPkgSeed-class000
AffyExpressionPDInfoPkgSeed-class000
AffySNPCNVPDInfoPkgSeed-class000
AffySNPCNVPDInfoPkgSeed2-class000
AffySNPPDInfoPkgSeed-class0.290.140.43
AffySNPPDInfoPkgSeed2-class000
AffySTPDInfoPkgSeed-class000
AffyTilingPDInfoPkgSeed-class0.000.020.02
NgsExpressionPDInfoPkgSeed-class000
NgsTilingPDInfoPkgSeed-class000
NimbleGenPDInfoPkgSeed-class000
makePdInfoPackage000

pdInfoBuilder.Rcheck/examples_x64/pdInfoBuilder-Ex.timings

nameusersystemelapsed
AffyClariomSPDInfoPkgSeed-class000
AffyExpressionPDInfoPkgSeed-class000
AffySNPCNVPDInfoPkgSeed-class000
AffySNPCNVPDInfoPkgSeed2-class000
AffySNPPDInfoPkgSeed-class0.410.010.42
AffySNPPDInfoPkgSeed2-class000
AffySTPDInfoPkgSeed-class000
AffyTilingPDInfoPkgSeed-class000
NgsExpressionPDInfoPkgSeed-class000
NgsTilingPDInfoPkgSeed-class000
NimbleGenPDInfoPkgSeed-class000
makePdInfoPackage000