BioC 3.0: CHECK report for customProDB on zin1
This page was generated on 2015-04-10 09:40:57 -0700 (Fri, 10 Apr 2015).
customProDB 1.6.0
xiaojing wang
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/customProDB | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
Summary
| Package: customProDB |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings customProDB_1.6.0.tar.gz |
| StartedAt: 2015-04-09 23:03:20 -0700 (Thu, 09 Apr 2015) |
| EndedAt: 2015-04-09 23:09:32 -0700 (Thu, 09 Apr 2015) |
| EllapsedTime: 372.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: customProDB.Rcheck |
| Warnings: 1 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings customProDB_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/customProDB.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.6.0’
* 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 ‘customProDB’ can be installed ... [24s/24s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘IRanges’ ‘biomaRt’ ‘AnnotationDbi’
A package should be listed in only one of these fields.
* 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’
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
.parseBMMartParams: no visible global function definition for
‘isSingleString’
Bed2Range: no visible binding for global variable ‘V5’
InputVcf: no visible global function definition for ‘DataFrame’
InputVcf: no visible binding for global variable ‘DataFrame’
InputVcf : <anonymous>: no visible global function definition for
‘DataFrame’
OutputNovelJun: no visible binding for global variable ‘jun_type’
OutputVarproseq: no visible binding for global variable ‘genename’
OutputVarproseq: no visible binding for global variable ‘txname’
OutputVarproseq: no visible binding for global variable ‘proname’
OutputVarproseq: no visible binding for global variable ‘aaref’
OutputVarproseq: no visible binding for global variable ‘aapos’
OutputVarproseq: no visible binding for global variable ‘aavar’
OutputVarproseq: no visible binding for global variable ‘rsid’
OutputVarproseq_single: no visible binding for global variable
‘genename’
OutputVarproseq_single: no visible binding for global variable ‘txname’
OutputVarproseq_single: no visible binding for global variable
‘proname’
OutputVarproseq_single: no visible binding for global variable ‘aaref’
OutputVarproseq_single: no visible binding for global variable ‘aapos’
OutputVarproseq_single: no visible binding for global variable ‘aavar’
OutputVarproseq_single: no visible binding for global variable ‘rsid’
Outputaberrant: no visible binding for global variable ‘pro_name’
Positionincoding: no visible binding for global variable ‘cds_start’
Positionincoding: no visible binding for global variable ‘cds_end’
PrepareAnnotationEnsembl: no visible global function definition for
‘genome<-’
PrepareAnnotationEnsembl: no visible binding for global variable
‘ensembl_gene_id’
PrepareAnnotationEnsembl: no visible binding for global variable
‘pro_name’
PrepareAnnotationEnsembl: no visible binding for global variable
‘tx_name’
PrepareAnnotationEnsembl: no visible binding for global variable
‘chrom’
PrepareAnnotationEnsembl: no visible binding for global variable ‘name’
PrepareAnnotationEnsembl: no visible binding for global variable
‘alleleCount’
PrepareAnnotationEnsembl: no visible binding for global variable
‘alleles’
PrepareAnnotationRefseq: no visible global function definition for
‘genome<-’
PrepareAnnotationRefseq: no visible binding for global variable
‘mrnaAcc’
PrepareAnnotationRefseq: no visible binding for global variable ‘name’
PrepareAnnotationRefseq: no visible binding for global variable
‘protAcc’
PrepareAnnotationRefseq: no visible binding for global variable
‘transcript’
PrepareAnnotationRefseq: no visible binding for global variable ‘chrom’
PrepareAnnotationRefseq: no visible binding for global variable
‘alleleCount’
PrepareAnnotationRefseq: no visible binding for global variable
‘alleles’
SharedJunc: no visible binding for global variable ‘allsample’
Varlocation: no visible binding for global variable ‘pro_name’
calculateRPKM: no visible global function definition for
‘keepSeqlevels’
joinDataFrameWithName2Val: no visible global function definition for
‘isSingleString’
setDataFrameColClass: no visible global function definition for
‘isTRUEorFALSE’
* 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 ... [60s/139s] WARNING
Found the following significant warnings:
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
PrepareAnnotationRefseq 25.994 0.248 82.737
PrepareAnnotationEnsembl 1.732 0.064 23.682
* 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
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/customProDB.Rcheck/00check.log’
for details.
customProDB.Rcheck/00install.out:
* installing *source* package ‘customProDB’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (customProDB)
customProDB.Rcheck/customProDB-Ex.timings:
| name | user | system | elapsed
|
| Bed2Range | 0.080 | 0.004 | 0.087 |
|
| InputVcf | 0.660 | 0.020 | 0.682 |
|
| JunctionType | 1.420 | 0.000 | 1.422 |
|
| Multiple_VCF | 0.956 | 0.028 | 0.983 |
|
| OutputNovelJun | 2.329 | 0.028 | 2.388 |
|
| OutputVarproseq | 0.816 | 0.008 | 0.824 |
|
| OutputVarproseq_single | 0.744 | 0.012 | 0.755 |
|
| Outputaberrant | 0.392 | 0.004 | 0.397 |
|
| Outputproseq | 0.948 | 0.016 | 1.003 |
|
| OutputsharedPro | 2.856 | 0.008 | 2.911 |
|
| Positionincoding | 0.540 | 0.008 | 0.550 |
|
| PrepareAnnotationEnsembl | 1.732 | 0.064 | 23.682 |
|
| PrepareAnnotationRefseq | 25.994 | 0.248 | 82.737 |
|
| SharedJunc | 0.808 | 0.008 | 0.818 |
|
| Varlocation | 0.000 | 0.000 | 0.001 |
|
| aaVariation | 0.740 | 0.000 | 0.744 |
|
| calculateRPKM | 0.880 | 0.004 | 0.886 |
|
| easyRun | 1.876 | 0.004 | 1.884 |
|
| easyRun_mul | 4.372 | 0.004 | 4.416 |
|