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CHECK report for PGA on celaya2

This page was generated on 2019-10-16 12:55:52 -0400 (Wed, 16 Oct 2019).

Package 1198/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PGA 1.14.0
Bo Wen , Shaohang Xu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PGA
Branch: RELEASE_3_9
Last Commit: 48259d4
Last Changed Date: 2019-05-02 11:53:55 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

PGA.Rcheck/00install.out

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


* 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)

Tests output

PGA.Rcheck/tests/runTests.Rout


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 

Example timings

PGA.Rcheck/PGA-Ex.timings

nameusersystemelapsed
PrepareAnnotationEnsembl2 5.002 0.31820.511
PrepareAnnotationRefseq20.0010.0000.001
addGeneName4Ensembl0.0010.0000.001
createProDB4DenovoRNASeq2.8521.0211.970
dbCreator47.242 3.25844.615
easyRun47.35611.77740.419
parserGear28.070 5.76823.114
reportGear45.26210.70138.723
runTandem19.397 1.94716.835