Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:25:13 -0400 (Wed, 17 Oct 2018).
Package 333/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
customProDB 1.20.2 Xiaojing Wang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: customProDB |
Version: 1.20.2 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings customProDB_1.20.2.tar.gz |
StartedAt: 2018-10-15 23:36:09 -0400 (Mon, 15 Oct 2018) |
EndedAt: 2018-10-15 23:39:43 -0400 (Mon, 15 Oct 2018) |
EllapsedTime: 213.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: customProDB.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings customProDB_1.20.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/customProDB.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-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 ‘1.20.2’ * 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 ‘customProDB’ can be installed ... OK * checking installed package size ... OK * 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’ 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 Bed2Range: no visible binding for global variable ‘V5’ 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 binding for global variable ‘ensembl_gene_id’ PrepareAnnotationEnsembl: no visible binding for global variable ‘pro_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 binding for global variable ‘name’ PrepareAnnotationRefseq: no visible binding for global variable ‘mrnaAcc’ 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’ PrepareAnnotationRefseq: no visible binding for global variable ‘COSMIC’ Varlocation: no visible binding for global variable ‘pro_name’ Undefined global functions or variables: COSMIC V5 aapos aaref aavar alleleCount alleles cds_end cds_start chrom ensembl_gene_id genename jun_type mrnaAcc name pro_name proname protAcc rsid transcript txname * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed PrepareAnnotationEnsembl 3.112 0.028 27.738 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/customProDB.Rcheck/00check.log’ for details.
customProDB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL customProDB ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘customProDB’ ... ** 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 * DONE (customProDB)
customProDB.Rcheck/customProDB-Ex.timings
name | user | system | elapsed | |
Bed2Range | 0.068 | 0.004 | 0.079 | |
InputVcf | 0.576 | 0.036 | 0.800 | |
JunctionType | 1.276 | 0.048 | 1.341 | |
Multiple_VCF | 0.476 | 0.044 | 0.531 | |
OutputNovelJun | 1.344 | 0.000 | 1.377 | |
OutputVarprocodingseq | 0.500 | 0.004 | 0.521 | |
OutputVarproseq | 0.472 | 0.008 | 0.481 | |
OutputVarproseq_single | 0.480 | 0.008 | 0.490 | |
Outputaberrant | 0.216 | 0.012 | 0.232 | |
Outputproseq | 0.676 | 0.004 | 0.713 | |
OutputsharedPro | 1.580 | 0.004 | 1.604 | |
Positionincoding | 0.416 | 0.004 | 0.436 | |
PrepareAnnotationEnsembl | 3.112 | 0.028 | 27.738 | |
PrepareAnnotationRefseq | 0.000 | 0.000 | 0.001 | |
SharedJunc | 0.512 | 0.004 | 0.533 | |
Varlocation | 0.000 | 0.000 | 0.001 | |
aaVariation | 0.496 | 0.000 | 0.497 | |
calculateRPKM | 0.564 | 0.004 | 0.569 | |
easyRun | 1.220 | 0.000 | 1.221 | |
easyRun_mul | 2.488 | 0.004 | 2.494 | |