Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:13:47 -0400 (Thu, 12 Apr 2018).
Package 1025/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
PGA 1.8.1 Bo Wen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: PGA |
Version: 1.8.1 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PGA_1.8.1.tar.gz |
StartedAt: 2018-04-12 01:46:13 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 01:51:19 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 306.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PGA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PGA_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PGA.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (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 ‘1.8.1’ * 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 for sufficient/correct file permissions ... 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 * 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 ... OK Examples with CPU or elapsed time > 5s user system elapsed easyRun 22.184 0.444 19.885 reportGear 18.376 0.564 15.682 dbCreator 14.572 0.136 14.570 parserGear 13.940 0.520 10.146 runTandem 9.744 0.140 9.712 PrepareAnnotationEnsembl2 6.524 0.112 29.619 * 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 ‘/home/biocbuild/bbs-3.6-bioc/meat/PGA.Rcheck/00check.log’ for details.
PGA.Rcheck/00install.out
* 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 * DONE (PGA)
PGA.Rcheck/tests/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-pc-linux-gnu (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 01:51:17 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 9.668 0.132 9.804
PGA.Rcheck/PGA-Ex.timings
name | user | system | elapsed | |
PrepareAnnotationEnsembl2 | 6.524 | 0.112 | 29.619 | |
PrepareAnnotationRefseq2 | 0.000 | 0.000 | 0.001 | |
addGeneName4Ensembl | 0.000 | 0.000 | 0.001 | |
createProDB4DenovoRNASeq | 1.708 | 0.004 | 1.650 | |
dbCreator | 14.572 | 0.136 | 14.570 | |
easyRun | 22.184 | 0.444 | 19.885 | |
parserGear | 13.940 | 0.520 | 10.146 | |
reportGear | 18.376 | 0.564 | 15.682 | |
runTandem | 9.744 | 0.140 | 9.712 | |