BioC 3.4: CHECK report for PGA on moscato1

Package: PGA

Version: 1.3.15

Command: rm -rf PGA.buildbin-libdir PGA.Rcheck && mkdir PGA.buildbin-libdir PGA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGA.buildbin-libdir PGA_1.3.15.tar.gz >PGA.Rcheck\00install.out 2>&1 && cp PGA.Rcheck\00install.out PGA-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PGA.buildbin-libdir --install="check:PGA-install.out" --force-multiarch --no-vignettes --timings PGA_1.3.15.tar.gz

StartedAt: 2016-09-20 13:51:15 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 14:05:32 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 856.8 seconds

RetCode: 0

Status:  OK

CheckDir: PGA.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf PGA.buildbin-libdir PGA.Rcheck && mkdir PGA.buildbin-libdir PGA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGA.buildbin-libdir PGA_1.3.15.tar.gz >PGA.Rcheck\00install.out 2>&1 && cp PGA.Rcheck\00install.out PGA-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PGA.buildbin-libdir --install="check:PGA-install.out" --force-multiarch --no-vignettes --timings PGA_1.3.15.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/PGA.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 'PGA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGA' version '1.3.15'
* 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 'PGA' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
* 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
Unexported objects imported by ':::' calls:
  'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
  'customProDB:::makeTranscriptDbFromBiomart_archive'
  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
.base_transfer: no visible binding for global variable 'peptide'
.base_transfer: no visible binding for global variable 'refbase'
.base_transfer: no visible binding for global variable 'varbase'
.base_transfer: no visible binding for global variable 'aaref'
.base_transfer: no visible binding for global variable 'aavar'
.base_transfer: no visible binding for global variable 'Type'
.base_transfer: no visible binding for global variable 'Freq'
.get_30aa_splited_seq: no visible global function definition for '.'
.get_30aa_splited_seq: no visible binding for global variable 'id'
.get_30aa_splited_seq: no visible binding for global variable 'cumlen'
.get_30aa_splited_seq: no visible binding for global variable
  'Substring'
.get_30aa_splited_seq: no visible binding for global variable '.N'
.juc_type: no visible binding for global variable 'peptide'
.juc_type: no visible binding for global variable 'jun_type'
.juc_type: no visible binding for global variable 'Type'
.juc_type: no visible binding for global variable 'Freq'
.mut_count_pro: no visible binding for global variable 'proname'
.mut_count_pro: no visible binding for global variable 'aaref'
.mut_count_pro: no visible binding for global variable 'aapos'
.mut_count_pro: no visible binding for global variable 'aavar'
.mut_count_pro: no visible binding for global variable 'MutNum'
.mut_count_pro: no visible binding for global variable 'Freq'
.mut_freq_heatmap: no visible binding for global variable 'peptide'
.mut_freq_heatmap: no visible binding for global variable 'aaref'
.mut_freq_heatmap: no visible binding for global variable 'aavar'
.peptide_number_of_ntx: no visible binding for global variable
  'peptide'
.peptide_number_of_ntx: no visible binding for global variable 'id'
.peptide_number_of_ntx: no visible binding for global variable 'ID'
.peptide_number_of_ntx: no visible binding for global variable 'Freq'
.wm_evalue_hist: no visible binding for global variable 'Evalue'
.wm_evalue_hist: no visible binding for global variable 'Class'
.wm_mass_hist: no visible binding for global variable 'Mass'
.wm_mass_hist: no visible binding for global variable 'Class'
OutputNovelJun2: no visible binding for global variable 'jun_type'
OutputNovelJun2: no visible global function definition for 'subseq'
OutputVarproseq2: no visible binding for global variable 'Index'
OutputVarproseq2: no visible binding for global variable 'genename'
OutputVarproseq2: no visible binding for global variable 'txname'
OutputVarproseq2: no visible binding for global variable 'proname'
OutputVarproseq2: no visible binding for global variable 'aaref'
OutputVarproseq2: no visible binding for global variable 'aapos'
OutputVarproseq2: no visible binding for global variable 'aavar'
OutputVarproseq2: no visible binding for global variable 'rsid'
Outputaberrant2: no visible binding for global variable 'pro_name'
Outputaberrant2: no visible binding for global variable 'Index'
Outputaberrant2: no visible binding for global variable 'txid'
Outputaberrant2: no visible binding for global variable 'genename'
Outputaberrant2: no visible binding for global variable 'txname'
Outputaberrant2: no visible binding for global variable 'proname'
Outputaberrant2: no visible binding for global variable 'chr'
Outputaberrant2: no visible binding for global variable 'refbase'
Outputaberrant2: no visible binding for global variable 'varbase'
Outputaberrant2: no visible binding for global variable 'pincoding'
Outputaberrant2: no visible binding for global variable 'gene_name'
Outputaberrant2: no visible binding for global variable 'tx_name'
PrepareAnnotationEnsembl2: no visible global function definition for
  'genome<-'
PrepareAnnotationEnsembl2: no visible binding for global variable
  'pro_name'
PrepareAnnotationEnsembl2: no visible binding for global variable
  'tx_name'
PrepareAnnotationEnsembl2: no visible binding for global variable
  'chrom'
PrepareAnnotationEnsembl2: no visible binding for global variable
  'name'
PrepareAnnotationEnsembl2: no visible binding for global variable
  'alleleCount'
PrepareAnnotationEnsembl2: no visible binding for global variable
  'alleles'
PrepareAnnotationRefseq2: no visible global function definition for
  'genome<-'
PrepareAnnotationRefseq2: no visible binding for global variable
  'mrnaAcc'
PrepareAnnotationRefseq2: no visible binding for global variable 'name'
PrepareAnnotationRefseq2: no visible binding for global variable
  'protAcc'
PrepareAnnotationRefseq2: no visible global function definition for
  'readAAStringSet'
PrepareAnnotationRefseq2: no visible global function definition for
  'readDNAStringSet'
PrepareAnnotationRefseq2: no visible binding for global variable
  'transcript'
PrepareAnnotationRefseq2: no visible binding for global variable
  'chrom'
PrepareAnnotationRefseq2: no visible binding for global variable
  'alleleCount'
PrepareAnnotationRefseq2: no visible binding for global variable
  'alleles'
createProDB4DenovoRNASeq: no visible global function definition for
  'readDNAStringSet'
createProDB4DenovoRNASeq: no visible global function definition for
  'subseq'
createProDB4DenovoRNASeq: no visible binding for global variable 'id'
createProDB4DenovoRNASeq: no visible binding for global variable
  'Substring'
createProDB4DenovoRNASeq: no visible global function definition for '.'
createProDB4DenovoRNASeq: no visible global function definition for
  'rbindlist'
createProDB4DenovoRNASeq: no visible binding for global variable
  'Index'
createProDB4DenovoRNASeq: no visible binding for global variable '.I'
createProDB4DenovoRNASeq: no visible binding for global variable 'ID'
createProDB4DenovoRNASeq: no visible binding for global variable
  'Strand'
createProDB4DenovoRNASeq: no visible binding for global variable
  'Frame'
createProDB4DenovoRNASeq: no visible binding for global variable
  'output'
createProDB4DenovoRNASeq: no visible binding for global variable 'pep'
createProDB4DenovoRNASeq: no visible global function definition for
  'readAAStringSet'
createProDB4DenovoRNASeq: no visible global function definition for
  'writeXStringSet'
dbcat: no visible global function definition for 'readAAStringSet'
dbcat: no visible global function definition for 'writeXStringSet'
getNovelTx: no visible global function definition for 'seqlengths'
getNovelTx: no visible global function definition for 'seqlevels'
getNovelTx: no visible global function definition for 'seqlevels<-'
getNovelTx: no visible global function definition for 'subseq'
getNovelTx: no visible binding for global variable 'id'
getNovelTx: no visible binding for global variable 'Substring'
getNovelTx: no visible global function definition for '.'
getNovelTx: no visible global function definition for 'rbindlist'
getNovelTx: no visible binding for global variable 'Index'
getNovelTx: no visible binding for global variable '.I'
getNovelTx: no visible binding for global variable 'ID'
getNovelTx: no visible binding for global variable 'Strand'
getNovelTx: no visible binding for global variable 'Frame'
getNovelTx: no visible binding for global variable 'output'
getNovelTx: no visible binding for global variable 'pep'
mybarplot: no visible binding for global variable 'x'
mybarplot: no visible binding for global variable 'y'
mybarplot: no visible binding for global variable 'label'
reportIDL: no visible binding for global variable 'isSAP'
reportIDL: no visible binding for global variable 'protein'
reportIDL: no visible global function definition for '.'
reportIDL: no visible binding for global variable 'Query'
reportIDL: no visible binding for global variable 'evalue'
reportIDL: no visible binding for global variable 'charge'
reportIDL: no visible binding for global variable 'mz'
reportIDL: no visible binding for global variable 'delta_da'
reportIDL: no visible binding for global variable 'delta_ppm'
reportIDL: no visible binding for global variable 'peptide'
reportIDL: no visible binding for global variable 'miss'
reportIDL: no visible binding for global variable 'mods'
reportIDL: no visible binding for global variable 'Qvalue'
reportIDL: no visible binding for global variable 'isUnique'
reportIDL: no visible binding for global variable 'prot'
reportIDL: no visible binding for global variable 'Index'
reportIDL: no visible binding for global variable 'genename'
reportIDL: no visible binding for global variable 'proname'
reportIDL: no visible binding for global variable '.SD'
reportIDL: no visible binding for global variable 'ID'
reportIDL: no visible binding for global variable 'Change'
reportJUC: no visible binding for global variable 'isSAP'
reportJUC: no visible binding for global variable 'protein'
reportJUC: no visible global function definition for '.'
reportJUC: no visible binding for global variable 'position'
reportJUC: no visible binding for global variable 'Query'
reportJUC: no visible binding for global variable 'evalue'
reportJUC: no visible binding for global variable 'charge'
reportJUC: no visible binding for global variable 'mz'
reportJUC: no visible binding for global variable 'delta_da'
reportJUC: no visible binding for global variable 'delta_ppm'
reportJUC: no visible binding for global variable 'peptide'
reportJUC: no visible binding for global variable 'miss'
reportJUC: no visible binding for global variable 'mods'
reportJUC: no visible binding for global variable 'Qvalue'
reportJUC: no visible binding for global variable 'isUnique'
reportJUC: no visible binding for global variable 'prot'
reportJUC: no visible binding for global variable 'Index'
reportJUC: no visible binding for global variable 'jun_type'
reportJUC: no visible binding for global variable 'id'
reportJUC: no visible binding for global variable '.SD'
reportJUC: no visible binding for global variable 'ID'
reportJUC: no visible binding for global variable 'junType'
reportNTX: no visible binding for global variable 'isSAP'
reportNTX: no visible binding for global variable 'protein'
reportNTX: no visible global function definition for '.'
reportNTX: no visible binding for global variable 'Query'
reportNTX: no visible binding for global variable 'evalue'
reportNTX: no visible binding for global variable 'charge'
reportNTX: no visible binding for global variable 'mz'
reportNTX: no visible binding for global variable 'delta_da'
reportNTX: no visible binding for global variable 'delta_ppm'
reportNTX: no visible binding for global variable 'peptide'
reportNTX: no visible binding for global variable 'miss'
reportNTX: no visible binding for global variable 'mods'
reportNTX: no visible binding for global variable 'Qvalue'
reportNTX: no visible binding for global variable 'isUnique'
reportNTX: no visible binding for global variable 'prot'
reportNTX: no visible binding for global variable 'Index'
reportNTX: no visible binding for global variable 'id'
reportNTX: no visible binding for global variable 'Frame'
reportNTX: no visible binding for global variable '.SD'
reportNTX: no visible binding for global variable 'ID'
reportNTX: no visible binding for global variable 'CUFF_ID'
reportSNV: no visible binding for global variable 'isSAP'
reportSNV: no visible binding for global variable 'protein'
reportSNV: no visible global function definition for '.'
reportSNV: no visible binding for global variable 'position'
reportSNV: no visible binding for global variable 'Query'
reportSNV: no visible binding for global variable 'evalue'
reportSNV: no visible binding for global variable 'charge'
reportSNV: no visible binding for global variable 'mz'
reportSNV: no visible binding for global variable 'delta_da'
reportSNV: no visible binding for global variable 'delta_ppm'
reportSNV: no visible binding for global variable 'peptide'
reportSNV: no visible binding for global variable 'miss'
reportSNV: no visible binding for global variable 'mods'
reportSNV: no visible binding for global variable 'Qvalue'
reportSNV: no visible binding for global variable 'prot'
reportSNV: no visible binding for global variable 'isUnique'
reportSNV: no visible binding for global variable 'Index'
reportSNV: no visible binding for global variable 'aaref'
reportSNV: no visible binding for global variable 'aavar'
reportSNV: no visible binding for global variable 'genename'
reportSNV: no visible binding for global variable 'proname'
reportSNV: no visible binding for global variable '.SD'
reportSNV: no visible binding for global variable 'ID'
reportSNV: no visible binding for global variable 'Change'
reportSNV: no visible binding for global variable 'aapos'
reportSNV: no visible binding for global variable 'abc'
reportSNV: no visible binding for global variable 'xyz'
Undefined global functions or variables:
  . .I .N .SD CUFF_ID Change Class Evalue Frame Freq ID Index Mass
  MutNum Query Qvalue Strand Substring Type aapos aaref aavar abc
  alleleCount alleles charge chr chrom cumlen delta_da delta_ppm evalue
  gene_name genename genome<- id isSAP isUnique junType jun_type label
  miss mods mrnaAcc mz name output pep peptide pincoding position
  pro_name proname prot protAcc protein rbindlist readAAStringSet
  readDNAStringSet refbase rsid seqlengths seqlevels seqlevels<- subseq
  transcript tx_name txid txname varbase writeXStringSet x xyz y
* 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
PrepareAnnotationRefseq2  22.42   0.44  162.53
easyRun                   15.18   1.42   19.97
reportGear                14.37   1.09   17.30
dbCreator                  9.03   0.12    9.28
runTandem                  8.79   0.14    8.66
parserGear                 8.24   0.05   11.87
PrepareAnnotationEnsembl2  5.19   0.34   28.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
PrepareAnnotationRefseq2  21.41   0.30  148.35
reportGear                16.68   1.53   24.30
easyRun                   15.87   1.20   20.67
parserGear                 9.47   0.05   13.47
dbCreator                  8.94   0.09    9.38
runTandem                  8.86   0.09    8.77
PrepareAnnotationEnsembl2  6.42   0.48   30.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/PGA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'PGA' ...
** 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 'PGA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PGA' as PGA_1.3.15.zip
* DONE (PGA)

name	user	system	elapsed
PrepareAnnotationEnsembl2	5.19	0.34	28.83
PrepareAnnotationRefseq2	22.42	0.44	162.53
addGeneName4Ensembl	0	0	0
createProDB4DenovoRNASeq	1.45	0.02	1.54
dbCreator	9.03	0.12	9.28
easyRun	15.18	1.42	19.97
parserGear	8.24	0.05	11.87
reportGear	14.37	1.09	17.30
runTandem	8.79	0.14	8.66

name	user	system	elapsed
PrepareAnnotationEnsembl2	6.42	0.48	30.00
PrepareAnnotationRefseq2	21.41	0.30	148.35
addGeneName4Ensembl	0	0	0
createProDB4DenovoRNASeq	0.98	0.03	1.03
dbCreator	8.94	0.09	9.38
easyRun	15.87	1.20	20.67
parserGear	9.47	0.05	13.47
reportGear	16.68	1.53	24.30
runTandem	8.86	0.09	8.77