Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:38 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 451/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
customProDB 1.39.0 (landing page) Xiaojing Wang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: customProDB |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings customProDB_1.39.0.tar.gz |
StartedAt: 2023-02-28 00:58:44 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 01:12:17 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 813.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: customProDB.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings customProDB_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/customProDB.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘customProDB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘customProDB’ version ‘1.39.0’ * 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 ... 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 (user + system) or elapsed time > 5s user system elapsed PrepareAnnotationEnsembl 6.449 0.7 43.447 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘customProDB.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/customProDB.Rcheck/00check.log’ for details.
customProDB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL customProDB ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 0.100 | 0.016 | 0.117 | |
InputVcf | 0.836 | 0.036 | 0.873 | |
JunctionType | 1.021 | 0.048 | 1.071 | |
Multiple_VCF | 1.860 | 0.076 | 1.938 | |
OutputNovelJun | 1.673 | 0.152 | 1.825 | |
OutputVarprocodingseq | 0.734 | 0.028 | 0.763 | |
OutputVarproseq | 0.682 | 0.012 | 0.694 | |
OutputVarproseq_single | 0.725 | 0.020 | 0.745 | |
Outputaberrant | 0.374 | 0.012 | 0.386 | |
Outputproseq | 0.780 | 0.016 | 0.801 | |
OutputsharedPro | 2.178 | 0.036 | 2.221 | |
Positionincoding | 0.448 | 0.012 | 0.461 | |
PrepareAnnotationEnsembl | 6.449 | 0.700 | 43.447 | |
PrepareAnnotationRefseq | 0 | 0 | 0 | |
SharedJunc | 0.819 | 0.044 | 0.864 | |
Varlocation | 0.000 | 0.001 | 0.000 | |
aaVariation | 0.698 | 0.059 | 0.757 | |
calculateRPKM | 0.762 | 0.068 | 0.829 | |
easyRun | 1.758 | 0.080 | 1.838 | |
easyRun_mul | 4.040 | 0.164 | 4.204 | |