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CHECK report for pdInfoBuilder on malbec2

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 1288/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pdInfoBuilder 1.52.0
Benilton Carvalho
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/pdInfoBuilder
Branch: RELEASE_3_11
Last Commit: a4c3e8e
Last Changed Date: 2020-04-27 14:14:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### 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
###
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* 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.



Installation output

pdInfoBuilder.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL pdInfoBuilder
###
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* 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)

Tests output


Example timings

pdInfoBuilder.Rcheck/pdInfoBuilder-Ex.timings

nameusersystemelapsed
AffyClariomSPDInfoPkgSeed-class0.0030.0000.003
AffyExpressionPDInfoPkgSeed-class0.0010.0000.001
AffySNPCNVPDInfoPkgSeed-class0.0020.0000.002
AffySNPCNVPDInfoPkgSeed2-class0.0010.0000.001
AffySNPPDInfoPkgSeed-class0.5050.0040.508
AffySNPPDInfoPkgSeed2-class0.0010.0000.001
AffySTPDInfoPkgSeed-class0.0000.0010.002
AffyTilingPDInfoPkgSeed-class0.0000.0020.001
NgsExpressionPDInfoPkgSeed-class0.0000.0010.001
NgsTilingPDInfoPkgSeed-class0.0010.0000.002
NimbleGenPDInfoPkgSeed-class0.0010.0000.001
makePdInfoPackage000