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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:22 -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 1288/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pdInfoBuilder 1.52.0 Benilton Carvalho
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: pdInfoBuilder |
| Version: 1.52.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pdInfoBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.52.0.tar.gz |
| StartedAt: 2020-10-17 06:47:55 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:52:41 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 286.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pdInfoBuilder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pdInfoBuilder.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pdInfoBuilder_1.52.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.52.0'
* 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 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-3.11-bioc/R/library/pdInfoBuilder/libs/i386/pdInfoBuilder.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/meat/pdInfoBuilder.Rcheck/00check.log'
for details.
pdInfoBuilder.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pdInfoBuilder_1.52.0.tar.gz && rm -rf pdInfoBuilder.buildbin-libdir && mkdir pdInfoBuilder.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pdInfoBuilder.buildbin-libdir pdInfoBuilder_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pdInfoBuilder_1.52.0.zip && rm pdInfoBuilder_1.52.0.tar.gz pdInfoBuilder_1.52.0.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
100 359k 100 359k 0 0 4940k 0 --:--:-- --:--:-- --:--:-- 5450k
install for i386
* installing *source* package 'pdInfoBuilder' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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: 'dbListFields' when loading 'oligo'
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: 'dbListFields' when loading 'oligo'
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: '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
install for x64
* installing *source* package 'pdInfoBuilder' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/pdInfoBuilder.buildbin-libdir/pdInfoBuilder/libs/x64
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'pdInfoBuilder'
* MD5 sums
packaged installation of 'pdInfoBuilder' as pdInfoBuilder_1.52.0.zip
* DONE (pdInfoBuilder)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pdInfoBuilder' successfully unpacked and MD5 sums checked
|
pdInfoBuilder.Rcheck/examples_i386/pdInfoBuilder-Ex.timings
|
pdInfoBuilder.Rcheck/examples_x64/pdInfoBuilder-Ex.timings
|