BioC 3.5: CHECK report for GenomicFeatures on tokay2

Package: GenomicFeatures

Version: 1.28.4

Command: rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.28.4.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.28.4.tar.gz

StartedAt: 2017-08-16 00:01:29 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:32:15 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 1846.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicFeatures.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.28.4.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.28.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.28.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
  'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GenomicFeatures' 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
Unexported objects imported by ':::' calls:
  'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
  'rtracklayer:::resourceDescription' 'rtracklayer:::ucscTableOutputs'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.writeMetadataFeatureTable: no visible global function definition for
  'packageDescription'
.write_metadata_table: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'exonicParts' 'intronicParts'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
coordinate-mapping-methods 53.22   2.14  315.69
makeFeatureDbFromUCSC      35.89   3.61  154.24
coverageByTranscript       29.66   6.38   36.03
makeTxDbFromBiomart        18.80   0.82   66.18
extractTranscriptSeqs      14.45   0.25   15.03
makeTxDbFromUCSC            8.68   0.15  113.84
makeTxDbFromGFF             6.80   0.07    6.94
extractUpstreamSeqs         2.56   0.20   27.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
coordinate-mapping-methods 43.35   1.66   45.00
makeFeatureDbFromUCSC      36.93   2.53  156.16
coverageByTranscript       26.53   6.00   32.54
makeTxDbFromBiomart        21.71   0.78   84.30
extractTranscriptSeqs      14.24   0.14   14.38
makeTxDbFromUCSC            9.11   0.16  121.30
makeTxDbFromGFF             7.99   0.06    8.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GenomicFeatures' ...
** 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 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.28.4.zip
* DONE (GenomicFeatures)

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0	0	0
FeatureDb-class	0.09	0.01	0.11
TxDb-class	1.19	0.06	1.25
as-format-methods	1.62	0.08	1.70
coordinate-mapping-methods	53.22	2.14	315.69
coverageByTranscript	29.66	6.38	36.03
disjointExons	0	0	0
extractTranscriptSeqs	14.45	0.25	15.03
extractUpstreamSeqs	2.56	0.20	27.34
features	0.11	0.00	0.11
getPromoterSeq-methods	0.86	0.03	0.89
id2name	0.14	0.00	0.14
makeFeatureDbFromUCSC	35.89	3.61	154.24
makeTxDb	1.64	0.02	1.65
makeTxDbFromBiomart	18.80	0.82	66.18
makeTxDbFromGFF	6.80	0.07	6.94
makeTxDbFromGRanges	2.19	0.00	2.19
makeTxDbFromUCSC	8.68	0.15	113.84
makeTxDbPackage	0.33	0.02	2.78
mapIdsToRanges	0.74	0.00	0.74
mapRangesToIds	0.5	0.0	0.5
microRNAs	0	0	0
nearest-methods	0.57	0.03	0.61
select-methods	0.15	0.02	0.15
transcriptLengths	3.89	0.06	3.96
transcriptLocs2refLocs	3.65	0.08	3.73
transcripts	1.55	0.06	1.61
transcriptsBy	0.51	0.00	0.51
transcriptsByOverlaps	0.29	0.00	0.29

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0	0	0
FeatureDb-class	0.1	0.0	0.1
TxDb-class	1.64	0.00	1.64
as-format-methods	2.17	0.00	2.17
coordinate-mapping-methods	43.35	1.66	45.00
coverageByTranscript	26.53	6.00	32.54
disjointExons	0.01	0.00	0.01
extractTranscriptSeqs	14.24	0.14	14.38
extractUpstreamSeqs	1.87	0.06	1.93
features	0.08	0.00	0.08
getPromoterSeq-methods	0.83	0.02	0.84
id2name	0.21	0.00	0.22
makeFeatureDbFromUCSC	36.93	2.53	156.16
makeTxDb	1.57	0.00	1.57
makeTxDbFromBiomart	21.71	0.78	84.30
makeTxDbFromGFF	7.99	0.06	8.12
makeTxDbFromGRanges	3.03	0.00	3.03
makeTxDbFromUCSC	9.11	0.16	121.30
makeTxDbPackage	0.38	0.00	2.54
mapIdsToRanges	0.81	0.03	0.85
mapRangesToIds	0.63	0.00	0.62
microRNAs	0	0	0
nearest-methods	0.76	0.03	0.80
select-methods	0.21	0.00	0.20
transcriptLengths	4.51	0.06	4.58
transcriptLocs2refLocs	4.59	0.08	4.67
transcripts	1.90	0.03	1.92
transcriptsBy	0.56	0.00	0.57
transcriptsByOverlaps	0.32	0.00	0.31