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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:pdInfoBuilder.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings pdInfoBuilder_1.71.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/pdInfoBuilder.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pdInfoBuilder/DESCRIPTION’ ... OK
* this is package ‘pdInfoBuilder’ version ‘1.71.0’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 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 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
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 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/pdInfoBuilder.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL pdInfoBuilder
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘pdInfoBuilder’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)