BioC 2.13: CHECK report for GenomicFeatures on moscato1

Package: GenomicFeatures

Version: 1.14.5

Command: rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.14.5.tar.gz >GenomicFeatures-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.14.5.tar.gz && mv GenomicFeatures.buildbin-libdir/* GenomicFeatures.Rcheck/ && rmdir GenomicFeatures.buildbin-libdir

StartedAt: 2014-04-05 04:09:09 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:29:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 1244.5 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.14.5'
* 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 'GenomicFeatures' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'IRanges' 'GenomicRanges' 'rtracklayer' 'biomaRt' 'Biostrings'
A package should be listed in only one of these fields.
* 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
':::' calls which should be '::':
  'DBI:::dbGetQuery' 'DBI:::dbListFields' 'DBI:::dbListTables'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Biostrings:::getDNAComplementLookup' 'biomaRt:::martBM'
  'biomaRt:::martDataset' 'biomaRt:::martHost'
  'rtracklayer:::ucscTableOutputs'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.keys' '.reverseColAbbreviations'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.setseqnameStyle: no visible binding for global variable 'txdb'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'GenomicFeatures.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [298s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 109.44   6.73  122.91
makeFeatureDbFromUCSC          8.70   0.17   82.73
makeTranscriptDbFromUCSC       5.76   0.03   45.96
makeTranscriptDbFromBiomart    2.15   0.04   19.06
** running examples for arch 'x64' ... [319s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 112.78   9.83  122.62
makeFeatureDbFromUCSC         13.46   0.28   88.22
makeTranscriptDbFromUCSC       7.27   0.02   47.33
makeTranscriptDbFromBiomart    3.31   0.01   25.54
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'GenomicFeatures_unit_tests.R' [169s]
 [170s] OK
** running tests for arch 'x64'
  Running 'GenomicFeatures_unit_tests.R' [161s]
 [161s] 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-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_1.14.5.zip
* DONE (GenomicFeatures)

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0	0	0
FeatureDb-class	0.06	0.00	0.06
TranscriptDb-class	1.28	0.28	1.63
as-format-methods	1.91	0.00	1.90
extractTranscriptsFromGenome	109.44	6.73	122.91
features	0.09	0.00	0.09
getPromoterSeq-methods	3.90	0.21	4.53
id2name	0.11	0.00	0.11
makeFeatureDbFromUCSC	8.70	0.17	82.73
makeTranscriptDb	0.11	0.00	0.11
makeTranscriptDbFromBiomart	2.15	0.04	19.06
makeTranscriptDbFromGFF	2.00	0.07	2.06
makeTranscriptDbFromUCSC	5.76	0.03	45.96
makeTxDbPackage	0.43	0.00	0.79
nearest-methods	1.17	0.00	1.19
saveFeatures	0	0	0
select-methods	0.21	0.03	0.23
transcripts	2.78	0.00	2.78
transcriptsBy	1.98	0.02	1.99
transcriptsByOverlaps	0.41	0.01	0.42

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.01	0.00	0.01
FeatureDb-class	0.06	0.02	0.08
TranscriptDb-class	1.30	0.11	1.42
as-format-methods	2.36	0.00	2.36
extractTranscriptsFromGenome	112.78	9.83	122.62
features	0.11	0.01	0.12
getPromoterSeq-methods	3.79	0.22	4.01
id2name	0.11	0.02	0.13
makeFeatureDbFromUCSC	13.46	0.28	88.22
makeTranscriptDb	0.11	0.00	0.11
makeTranscriptDbFromBiomart	3.31	0.01	25.54
makeTranscriptDbFromGFF	2.65	0.08	2.73
makeTranscriptDbFromUCSC	7.27	0.02	47.33
makeTxDbPackage	0.46	0.03	0.49
nearest-methods	1.70	0.03	1.73
saveFeatures	0	0	0
select-methods	0.25	0.00	0.25
transcripts	3.95	0.02	3.96
transcriptsBy	2.60	0.00	2.61
transcriptsByOverlaps	0.64	0.00	0.63