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This page was generated on 2021-10-15 15:06:33 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the customProDB package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/customProDB.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 426/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
customProDB 1.32.0 (landing page) Xiaojing Wang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: customProDB |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:customProDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings customProDB_1.32.0.tar.gz |
StartedAt: 2021-10-14 17:58:23 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:04:21 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 358.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: customProDB.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:customProDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings customProDB_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/customProDB.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.32.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PrepareAnnotationEnsembl 12.031 0.26 25.889 easyRun_mul 5.230 0.06 5.295 * 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/customProDB.Rcheck/00check.log’ for details.
customProDB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL customProDB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘customProDB’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (customProDB)
customProDB.Rcheck/customProDB-Ex.timings
name | user | system | elapsed | |
Bed2Range | 0.912 | 0.003 | 0.916 | |
InputVcf | 1.174 | 0.123 | 1.299 | |
JunctionType | 1.165 | 0.070 | 1.237 | |
Multiple_VCF | 1.201 | 0.038 | 1.242 | |
OutputNovelJun | 2.137 | 0.048 | 2.189 | |
OutputVarprocodingseq | 0.850 | 0.009 | 0.860 | |
OutputVarproseq | 0.939 | 0.012 | 0.952 | |
OutputVarproseq_single | 0.874 | 0.014 | 0.888 | |
Outputaberrant | 0.461 | 0.014 | 0.476 | |
Outputproseq | 1.159 | 0.022 | 1.188 | |
OutputsharedPro | 3.066 | 0.019 | 3.092 | |
Positionincoding | 0.666 | 0.010 | 0.677 | |
PrepareAnnotationEnsembl | 12.031 | 0.260 | 25.889 | |
PrepareAnnotationRefseq | 0.000 | 0.000 | 0.001 | |
SharedJunc | 0.904 | 0.005 | 0.952 | |
Varlocation | 0 | 0 | 0 | |
aaVariation | 0.954 | 0.028 | 0.983 | |
calculateRPKM | 1.120 | 0.017 | 1.138 | |
easyRun | 2.075 | 0.021 | 2.097 | |
easyRun_mul | 5.230 | 0.060 | 5.295 | |