BioC 3.2: CHECK report for ELMER on moscato1

Package: ELMER

Version: 1.1.1

Command: rm -rf ELMER.buildbin-libdir ELMER.Rcheck && mkdir ELMER.buildbin-libdir ELMER.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ELMER.buildbin-libdir ELMER_1.1.1.tar.gz >ELMER.Rcheck\00install.out 2>&1 && cp ELMER.Rcheck\00install.out ELMER-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ELMER.buildbin-libdir --install="check:ELMER-install.out" --force-multiarch --no-vignettes --timings ELMER_1.1.1.tar.gz

StartedAt: 2015-08-20 04:03:28 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 04:19:50 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 981.3 seconds

RetCode: 0

Status:  OK

CheckDir: ELMER.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ELMER.buildbin-libdir ELMER.Rcheck && mkdir ELMER.buildbin-libdir ELMER.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ELMER.buildbin-libdir ELMER_1.1.1.tar.gz >ELMER.Rcheck\00install.out 2>&1 && cp ELMER.Rcheck\00install.out ELMER-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ELMER.buildbin-libdir --install="check:ELMER-install.out" --force-multiarch --no-vignettes --timings ELMER_1.1.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ELMER.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ELMER/DESCRIPTION' ... OK
* this is package 'ELMER' version '1.1.1'
* 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 'ELMER' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'ELMER.data' 'Homo.sapiens'
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TF.rank.plot: no visible binding for global variable 'pvalue'
TF.rank.plot: no visible binding for global variable 'label'
get.feature.probe: no visible binding for global variable
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'
motif.enrichment.plot: no visible binding for global variable 'upperOR'
motif.enrichment.plot: no visible binding for global variable 'lowerOR'
motif.enrichment.plot: no visible binding for global variable 'motif'
motif.enrichment.plot: no visible binding for global variable 'OR'
scatter: no visible binding for global variable 'value'
txs: no visible binding for global variable 'Homo.sapiens'
* 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' ... [127s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
get.feature.probe 16.66   0.55   17.20
get.pair          11.43   0.08   11.52
schematic.plot    11.41   0.00   11.41
GetNearGenes       9.88   0.17   10.09
get.permu          8.25   0.04    8.30
getGeneInfo        7.58   0.18    8.10
fetch.pair         7.43   0.09    7.52
scatter.plot       6.08   0.01    6.10
txs                5.57   0.08    5.65
getSymbol          5.46   0.09    5.56
getGeneID          5.37   0.07    5.46
** running examples for arch 'x64' ... [123s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
get.feature.probe 15.21   0.56   15.77
get.pair          11.65   0.14   11.81
schematic.plot    10.86   0.00   11.12
GetNearGenes       8.69   0.14    8.87
get.permu          8.11   0.05    8.16
getGeneInfo        7.71   0.09    7.80
fetch.pair         6.84   0.09    6.93
scatter.plot       6.46   0.02    7.16
txs                5.39   0.12    5.52
getGeneID          5.36   0.10    5.47
getSymbol          5.08   0.06    5.15
* 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-3.2-bioc/meat/ELMER.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ELMER' ...
** R
** inst
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly

install for x64

* installing *source* package 'ELMER' ...
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
* MD5 sums
packaged installation of 'ELMER' as ELMER_1.1.1.zip
* DONE (ELMER)

name	user	system	elapsed
GetNearGenes	9.88	0.17	10.09
TCGA.pipe	0	0	0
TF.rank.plot	0.69	0.00	0.69
fetch.mee	0.95	0.00	0.95
fetch.pair	7.43	0.09	7.52
get.TFs	0.73	0.03	2.98
get.diff.meth	0.81	0.00	0.81
get.enriched.motif	3.34	0.14	3.48
get.feature.probe	16.66	0.55	17.20
get.pair	11.43	0.08	11.52
get.permu	8.25	0.04	8.30
getExp	1.14	0.00	1.13
getGeneID	5.37	0.07	5.46
getGeneInfo	7.58	0.18	8.10
getMeth	1.33	0.00	1.33
getPair	0	0	0
getProbeInfo	1.25	0.00	1.25
getSample	1.23	0.00	1.23
getSymbol	5.46	0.09	5.56
getTCGA	0.00	0.02	0.68
motif.enrichment.plot	0.34	0.00	0.35
promoterMeth	0.30	0.00	0.29
scatter.plot	6.08	0.01	6.10
schematic.plot	11.41	0.00	11.41
txs	5.57	0.08	5.65

name	user	system	elapsed
GetNearGenes	8.69	0.14	8.87
TCGA.pipe	0	0	0
TF.rank.plot	0.77	0.00	0.88
fetch.mee	1.59	0.00	1.59
fetch.pair	6.84	0.09	6.93
get.TFs	0.84	0.04	0.89
get.diff.meth	0.33	0.06	0.81
get.enriched.motif	4.00	0.12	4.76
get.feature.probe	15.21	0.56	15.77
get.pair	11.65	0.14	11.81
get.permu	8.11	0.05	8.16
getExp	1.45	0.00	1.45
getGeneID	5.36	0.10	5.47
getGeneInfo	7.71	0.09	7.80
getMeth	1.38	0.00	1.39
getPair	0	0	0
getProbeInfo	1.36	0.00	1.35
getSample	1.33	0.00	1.33
getSymbol	5.08	0.06	5.15
getTCGA	0.02	0.00	0.12
motif.enrichment.plot	0.26	0.00	0.27
promoterMeth	0.30	0.03	0.33
scatter.plot	6.46	0.02	7.16
schematic.plot	10.86	0.00	11.12
txs	5.39	0.12	5.52