pdInfoBuilder 1.40.0
Benilton Carvalho
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/pdInfoBuilder | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pdInfoBuilder_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/pdInfoBuilder.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.40.0’
* 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 compiled code ... 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/pdInfoBuilder.Rcheck/00check.log’
for details.
* installing *source* package ‘pdInfoBuilder’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/pdInfoBuilder.Rcheck/pdInfoBuilder/libs
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (pdInfoBuilder)