BioC 3.4: CHECK report for AnnotationForge on moscato1

Package: AnnotationForge

Version: 1.15.10

Command: rm -rf AnnotationForge.buildbin-libdir AnnotationForge.Rcheck && mkdir AnnotationForge.buildbin-libdir AnnotationForge.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationForge.buildbin-libdir AnnotationForge_1.15.10.tar.gz >AnnotationForge.Rcheck\00install.out 2>&1 && cp AnnotationForge.Rcheck\00install.out AnnotationForge-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=AnnotationForge.buildbin-libdir --install="check:AnnotationForge-install.out" --force-multiarch --no-vignettes --timings AnnotationForge_1.15.10.tar.gz

StartedAt: 2016-09-20 03:52:59 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:57:56 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 297.1 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationForge.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf AnnotationForge.buildbin-libdir AnnotationForge.Rcheck && mkdir AnnotationForge.buildbin-libdir AnnotationForge.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationForge.buildbin-libdir AnnotationForge_1.15.10.tar.gz >AnnotationForge.Rcheck\00install.out 2>&1 && cp AnnotationForge.Rcheck\00install.out AnnotationForge-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=AnnotationForge.buildbin-libdir --install="check:AnnotationForge-install.out" --force-multiarch --no-vignettes --timings AnnotationForge_1.15.10.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/AnnotationForge.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationForge/DESCRIPTION' ... OK
* this is package 'AnnotationForge' version '1.15.10'
* 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 'AnnotationForge' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.3Mb
    extdata              3.3Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
listMappings: no visible global function definition for
  'NCBIORG_DB_SeedGenerator'
Undefined global functions or variables:
  NCBIORG_DB_SeedGenerator
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeProbePackage 4.57   0.03    7.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeProbePackage 4.71   0.05    5.97
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'AnnotationForge_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'AnnotationForge_unit_tests.R'
 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
  'D:/biocbld/bbs-3.4-bioc/meat/AnnotationForge.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'AnnotationForge' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'AnnotationForge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationForge' as AnnotationForge_1.15.10.zip
* DONE (AnnotationForge)

name	user	system	elapsed
AnnDbPkg-maker	0.05	0.00	0.05
available.db0pkgs	0.18	0.00	0.89
generateSeqnames_db	0	0	0
getProbeDataAffy	0	0	0
getProbeData_1lq	0	0	0
makeChipPackageFromDataFrames	0	0	0
makeInpDb	0	0	0
makeOrgPackage	0	0	0
makeOrgPackageFromDataFrames	0.02	0.00	0.01
makeProbePackage	4.57	0.03	7.35
sqlForge-makeCHIPDB	0	0	0
sqlForge-popDB	0	0	0
sqlForge-wrapDBPackages	0	0	0

name	user	system	elapsed
AnnDbPkg-maker	0.04	0.00	0.05
available.db0pkgs	0.22	0.03	0.24
generateSeqnames_db	0	0	0
getProbeDataAffy	0	0	0
getProbeData_1lq	0.00	0.02	0.01
makeChipPackageFromDataFrames	0	0	0
makeInpDb	0	0	0
makeOrgPackage	0	0	0
makeOrgPackageFromDataFrames	0	0	0
makeProbePackage	4.71	0.05	5.97
sqlForge-makeCHIPDB	0	0	0
sqlForge-popDB	0	0	0
sqlForge-wrapDBPackages	0	0	0