Package: PGA

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PGA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PGA_1.14.0.tar.gz

StartedAt: 2019-10-16 05:30:12 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:39:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 582.5 seconds

RetCode: 0

Status:  OK

CheckDir: PGA.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PGA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PGA_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PGA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PGA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PGA’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PGA’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  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
* 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’
  ‘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 ‘name’
PrepareAnnotationRefseq2: no visible binding for global variable
  ‘mrnaAcc’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
easyRun                   47.356 11.777  40.419
reportGear                45.262 10.701  38.723
dbCreator                 47.242  3.258  44.615
parserGear                28.070  5.768  23.114
runTandem                 19.397  1.947  16.835
PrepareAnnotationEnsembl2  5.002  0.318  20.511
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/PGA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PGA
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PGA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PGA)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("PGA")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'data.table'

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second



RUNIT TEST PROTOCOL -- Wed Oct 16 05:39:48 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PGA RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 17.780   1.401  19.137 

name	user	system	elapsed
PrepareAnnotationEnsembl2	5.002	0.318	20.511
PrepareAnnotationRefseq2	0.001	0.000	0.001
addGeneName4Ensembl	0.001	0.000	0.001
createProDB4DenovoRNASeq	2.852	1.021	1.970
dbCreator	47.242	3.258	44.615
easyRun	47.356	11.777	40.419
parserGear	28.070	5.768	23.114
reportGear	45.262	10.701	38.723
runTandem	19.397	1.947	16.835