PGA 1.2.2
Bo Wen , Shaohang Xu
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/PGA | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PGA_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/PGA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.2’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘data.table::shift’ by ‘IRanges::shift’ when loading ‘PGA’
See ‘/home/biocbuild/bbs-3.3-bioc/meat/PGA.Rcheck/00install.out’ for details.
* 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 global function definition for ‘read.delim’
.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’
.juc_type: no visible global function definition for ‘read.delim’
.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 global function definition for ‘read.delim’
.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 global function definition for
‘read.delim’
.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’
.mut_freq_heatmap: no visible global function definition for
‘colorRampPalette’
.peptide_number_of_ntx: no visible global function definition for
‘read.delim’
.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’
.precursor_error_hist: no visible global function definition for ‘par’
.precursor_error_hist: no visible global function definition for ‘hist’
.precursor_error_hist: no visible global function definition for
‘density’
.precursor_error_hist: no visible global function definition for ‘plot’
.precursor_error_hist: no visible global function definition for
‘colorRampPalette’
.precursor_error_hist: no visible global function definition for
‘abline’
.precursor_error_hist: no visible global function definition for
‘axTicks’
.precursor_error_hist: no visible global function definition for ‘clip’
.precursor_error_hist: no visible binding for global variable ‘clip’
.precursor_error_hist: no visible global function definition for
‘lines’
.precursor_error_hist: no visible global function definition for ‘rug’
.precursor_error_hist: no visible global function definition for ‘box’
.spplot: no visible global function definition for ‘pdf’
.spplot: no visible global function definition for ‘png’
.spplot: no visible global function definition for ‘par’
.spplot: no visible global function definition for ‘read.table’
.spplot: no visible global function definition for ‘plot’
.spplot: no visible global function definition for ‘mtext’
.spplot: no visible global function definition for ‘axis’
.spplot: no visible global function definition for ‘text’
.spplot: no visible global function definition for ‘abline’
.spplot: no visible global function definition for ‘lines’
.spplot: no visible global function definition for ‘points’
.spplot: no visible global function definition for ‘box’
.spplot: no visible global function definition for ‘dev.off’
.wm_charge_bar: no visible global function definition for ‘par’
.wm_charge_bar: no visible global function definition for ‘barplot’
.wm_charge_bar: no visible global function definition for ‘text’
.wm_charge_bar: no visible global function definition for ‘box’
.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’
OutputNovelJun2: no visible global function definition for
‘write.table’
OutputVarproseq2: no visible global function definition for
‘write.table’
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 global function definition for
‘write.table’
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’
Sys.which2: no visible global function definition for ‘setNames’
addGeneName4Ensembl: no visible global function definition for
‘read.delim’
addGeneName4Ensembl: no visible global function definition for
‘write.table’
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 binding for global variable
‘Index’
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 global function definition for
‘write.table’
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 binding for global variable ‘Index’
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 global function definition for ‘write.table’
getNovelTx: no visible binding for global variable ‘output’
getNovelTx: no visible binding for global variable ‘pep’
mybarplot: no visible global function definition for ‘png’
mybarplot: no visible binding for global variable ‘x’
mybarplot: no visible binding for global variable ‘y’
mybarplot: no visible binding for global variable ‘label’
mybarplot: no visible global function definition for ‘dev.off’
reportGear: no visible global function definition for ‘read.delim’
reportGear: no visible global function definition for ‘png’
reportGear: no visible global function definition for ‘dev.off’
reportGear: no visible global function definition for ‘par’
reportGear: no visible global function definition for ‘pie’
reportGear: no visible global function definition for ‘rainbow’
reportIDL: no visible binding for global variable ‘isSAP’
reportIDL: no visible global function definition for ‘read.delim’
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 ‘rt’
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 global function definition for ‘write.table’
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 global function definition for ‘read.delim’
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 ‘rt’
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 global function definition for ‘write.table’
reportJUC: no visible binding for global variable ‘ID’
reportJUC: no visible binding for global variable ‘junType’
reportJUC: no visible global function definition for ‘png’
reportJUC: no visible global function definition for ‘dev.off’
reportNTX: no visible binding for global variable ‘isSAP’
reportNTX: no visible global function definition for ‘read.delim’
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 ‘rt’
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 global function definition for ‘write.table’
reportNTX: no visible binding for global variable ‘ID’
reportNTX: no visible binding for global variable ‘CUFF_ID’
reportNTX: no visible global function definition for ‘png’
reportNTX: no visible global function definition for ‘dev.off’
reportSNV: no visible binding for global variable ‘isSAP’
reportSNV: no visible global function definition for ‘read.delim’
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 ‘rt’
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 global function definition for ‘write.table’
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’
reportSNV: no visible global function definition for ‘png’
reportSNV: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
. CUFF_ID Change Class Evalue Frame Freq ID Index Mass MutNum Query
Qvalue Strand Substring Type aapos aaref aavar abc abline alleleCount
alleles axTicks axis barplot box charge chr chrom clip
colorRampPalette cumlen delta_da delta_ppm density dev.off evalue
gene_name genename genome<- hist id isSAP isUnique junType jun_type
label lines miss mods mrnaAcc mtext mz name output par pdf pep
peptide pie pincoding plot png points position pro_name proname prot
protAcc protein rainbow read.delim read.table readAAStringSet
readDNAStringSet refbase rsid rt rug seqlengths seqlevels seqlevels<-
setNames subseq text transcript tx_name txid txname varbase
write.table writeXStringSet x xyz y
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "png",
"rainbow")
importFrom("graphics", "abline", "axTicks", "axis", "barplot", "box",
"clip", "hist", "lines", "mtext", "par", "pie", "plot",
"points", "rug", "text")
importFrom("stats", "density", "rt", "setNames")
importFrom("utils", "read.delim", "read.table", "write.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PGA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PrepareAnnotationEnsembl2
> ### Title: Prepare annotation from ENSEMBL
> ### Aliases: PrepareAnnotationEnsembl2
>
> ### ** Examples
>
> ensembl <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",
+ host="feb2012.archive.ensembl.org", path="/biomart/martservice",
+ archive=FALSE)
Entity 'nbsp' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'nbsp' not defined
Entity 'raquo' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Opening and ending tag mismatch: img line 68 and li
Opening and ending tag mismatch: li line 68 and ul
Opening and ending tag mismatch: ul line 67 and div
Entity 'copy' not defined
Opening and ending tag mismatch: div line 19 and body
Opening and ending tag mismatch: body line 17 and html
Premature end of data in tag html line 2
Error: 1: Entity 'nbsp' not defined
2: Entity 'hellip' not defined
3: Entity 'hellip' not defined
4: Entity 'nbsp' not defined
5: Entity 'raquo' not defined
6: Entity 'hellip' not defined
7: Entity 'hellip' not defined
8: Entity 'hellip' not defined
9: Entity 'hellip' not defined
10: Entity 'hellip' not defined
11: Opening and ending tag mismatch: img line 68 and li
12: Opening and ending tag mismatch: li line 68 and ul
13: Opening and ending tag mismatch: ul line 67 and div
14: Entity 'copy' not defined
15: Opening and ending tag mismatch: div line 19 and body
16: Opening and ending tag mismatch: body line 17 and html
17: Premature end of data in tag html line 2
Execution halted
* 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/PGA.Rcheck/00check.log’
for details.
* installing *source* package ‘PGA’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘data.table::shift’ by ‘IRanges::shift’ when loading ‘PGA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘data.table::shift’ by ‘IRanges::shift’ when loading ‘PGA’
* DONE (PGA)