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CHECK report for PGA on tokay1

This page was generated on 2018-04-12 13:26:28 -0400 (Thu, 12 Apr 2018).

Package 1025/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PGA 1.8.1
Bo Wen , Shaohang Xu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PGA
Branch: RELEASE_3_6
Last Commit: e2dbaf4
Last Changed Date: 2018-03-01 22:33:12 -0400 (Thu, 01 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PGA
Version: 1.8.1
Command: rm -rf PGA.buildbin-libdir PGA.Rcheck && mkdir PGA.buildbin-libdir PGA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGA.buildbin-libdir PGA_1.8.1.tar.gz >PGA.Rcheck\00install.out 2>&1 && cp PGA.Rcheck\00install.out PGA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PGA.buildbin-libdir --install="check:PGA-install.out" --force-multiarch --no-vignettes --timings PGA_1.8.1.tar.gz
StartedAt: 2018-04-12 02:07:02 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:16:27 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 564.9 seconds
RetCode: 0
Status:  OK  
CheckDir: PGA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PGA.buildbin-libdir PGA.Rcheck && mkdir PGA.buildbin-libdir PGA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGA.buildbin-libdir PGA_1.8.1.tar.gz >PGA.Rcheck\00install.out 2>&1 && cp PGA.Rcheck\00install.out PGA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PGA.buildbin-libdir --install="check:PGA-install.out" --force-multiarch --no-vignettes --timings PGA_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PGA.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.8.1'
* 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 'PGA' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  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
easyRun                   20.50   1.37   24.79
reportGear                16.40   1.43   18.71
dbCreator                 16.80   0.63   17.70
runTandem                  9.94   0.17    9.79
parserGear                 9.70   0.28   13.04
PrepareAnnotationEnsembl2  6.72   0.21   20.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
easyRun                   21.72   1.25   24.10
dbCreator                 19.08   0.17   19.42
reportGear                16.83   1.23   19.04
runTandem                 11.93   0.22   11.92
parserGear                11.81   0.13   13.69
PrepareAnnotationEnsembl2  8.17   0.19   23.22
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/PGA.Rcheck/00check.log'
for details.



Installation output

PGA.Rcheck/00install.out


install for i386

* installing *source* package 'PGA' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'PGA'
    finding HTML links ... done
    PrepareAnnotationEnsembl2               html  
    finding level-2 HTML links ... done

    PrepareAnnotationRefseq2                html  
    addGeneName4Ensembl                     html  
    createProDB4DenovoRNASeq                html  
    dbCreator                               html  
    easyRun                                 html  
    parserGear                              html  
    reportGear                              html  
    runTandem                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PGA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PGA' as PGA_1.8.1.zip
* DONE (PGA)
In R CMD INSTALL
In R CMD INSTALL

Tests output

PGA.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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 -- Thu Apr 12 02:16:12 2018 
*********************************************** 
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 
   9.39    0.34    9.71 

PGA.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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 -- Thu Apr 12 02:16:23 2018 
*********************************************** 
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 
  10.28    0.21   10.50 

Example timings

PGA.Rcheck/examples_i386/PGA-Ex.timings

nameusersystemelapsed
PrepareAnnotationEnsembl2 6.72 0.2120.81
PrepareAnnotationRefseq2000
addGeneName4Ensembl000
createProDB4DenovoRNASeq1.490.041.65
dbCreator16.80 0.6317.70
easyRun20.50 1.3724.79
parserGear 9.70 0.2813.04
reportGear16.40 1.4318.71
runTandem9.940.179.79

PGA.Rcheck/examples_x64/PGA-Ex.timings

nameusersystemelapsed
PrepareAnnotationEnsembl2 8.17 0.1923.22
PrepareAnnotationRefseq2000
addGeneName4Ensembl000
createProDB4DenovoRNASeq2.250.032.33
dbCreator19.08 0.1719.42
easyRun21.72 1.2524.10
parserGear11.81 0.1313.69
reportGear16.83 1.2319.04
runTandem11.93 0.2211.92