Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 470/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
customProDB 1.45.0 (landing page) Xiaojing Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the customProDB package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: customProDB |
Version: 1.45.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:customProDB.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings customProDB_1.45.0.tar.gz |
StartedAt: 2024-06-10 01:30:18 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 01:36:26 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 367.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: customProDB.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:customProDB.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings customProDB_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'customProDB/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'customProDB' version '1.45.0' * 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 whether package 'customProDB' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'GenomicFeatures::makeTxDbPackage' by 'txdbmaker::makeTxDbPackage' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTables' by 'txdbmaker::supportedUCSCFeatureDbTables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGFF' by 'txdbmaker::makeTxDbFromGFF' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromBiomart' by 'txdbmaker::makeTxDbPackageFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedMiRBaseBuildValues' by 'txdbmaker::supportedMiRBaseBuildValues' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTracks' by 'txdbmaker::supportedUCSCFeatureDbTracks' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::browseUCSCtrack' by 'txdbmaker::browseUCSCtrack' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::getChromInfoFromBiomart' by 'txdbmaker::getChromInfoFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGRanges' by 'txdbmaker::makeTxDbFromGRanges' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCtables' by 'txdbmaker::supportedUCSCtables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromBiomart' by 'txdbmaker::makeTxDbFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::UCSCFeatureDbTableSchema' by 'txdbmaker::UCSCFeatureDbTableSchema' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromEnsembl' by 'txdbmaker::makeTxDbFromEnsembl' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDb' by 'txdbmaker::makeTxDb' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFDbPackageFromUCSC' by 'txdbmaker::makeFDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromUCSC' by 'txdbmaker::makeTxDbFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromUCSC' by 'txdbmaker::makeTxDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makePackageName' by 'txdbmaker::makePackageName' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFeatureDbFromUCSC' by 'txdbmaker::makeFeatureDbFromUCSC' when loading 'customProDB' See 'F:/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck/00install.out' for details. * 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 code 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 5.55 1 12.78 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck/00check.log' for details.
customProDB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL customProDB ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'customProDB' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'GenomicFeatures::makeTxDbPackage' by 'txdbmaker::makeTxDbPackage' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTables' by 'txdbmaker::supportedUCSCFeatureDbTables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGFF' by 'txdbmaker::makeTxDbFromGFF' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromBiomart' by 'txdbmaker::makeTxDbPackageFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedMiRBaseBuildValues' by 'txdbmaker::supportedMiRBaseBuildValues' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTracks' by 'txdbmaker::supportedUCSCFeatureDbTracks' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::browseUCSCtrack' by 'txdbmaker::browseUCSCtrack' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::getChromInfoFromBiomart' by 'txdbmaker::getChromInfoFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGRanges' by 'txdbmaker::makeTxDbFromGRanges' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCtables' by 'txdbmaker::supportedUCSCtables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromBiomart' by 'txdbmaker::makeTxDbFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::UCSCFeatureDbTableSchema' by 'txdbmaker::UCSCFeatureDbTableSchema' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromEnsembl' by 'txdbmaker::makeTxDbFromEnsembl' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDb' by 'txdbmaker::makeTxDb' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFDbPackageFromUCSC' by 'txdbmaker::makeFDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromUCSC' by 'txdbmaker::makeTxDbFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromUCSC' by 'txdbmaker::makeTxDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makePackageName' by 'txdbmaker::makePackageName' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFeatureDbFromUCSC' by 'txdbmaker::makeFeatureDbFromUCSC' when loading 'customProDB' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'GenomicFeatures::makeTxDbPackage' by 'txdbmaker::makeTxDbPackage' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTables' by 'txdbmaker::supportedUCSCFeatureDbTables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGFF' by 'txdbmaker::makeTxDbFromGFF' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromBiomart' by 'txdbmaker::makeTxDbPackageFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedMiRBaseBuildValues' by 'txdbmaker::supportedMiRBaseBuildValues' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTracks' by 'txdbmaker::supportedUCSCFeatureDbTracks' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::browseUCSCtrack' by 'txdbmaker::browseUCSCtrack' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::getChromInfoFromBiomart' by 'txdbmaker::getChromInfoFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGRanges' by 'txdbmaker::makeTxDbFromGRanges' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCtables' by 'txdbmaker::supportedUCSCtables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromBiomart' by 'txdbmaker::makeTxDbFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::UCSCFeatureDbTableSchema' by 'txdbmaker::UCSCFeatureDbTableSchema' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromEnsembl' by 'txdbmaker::makeTxDbFromEnsembl' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDb' by 'txdbmaker::makeTxDb' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFDbPackageFromUCSC' by 'txdbmaker::makeFDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromUCSC' by 'txdbmaker::makeTxDbFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromUCSC' by 'txdbmaker::makeTxDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makePackageName' by 'txdbmaker::makePackageName' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFeatureDbFromUCSC' by 'txdbmaker::makeFeatureDbFromUCSC' when loading 'customProDB' ** testing if installed package can be loaded from final location Warning: replacing previous import 'GenomicFeatures::makeTxDbPackage' by 'txdbmaker::makeTxDbPackage' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTables' by 'txdbmaker::supportedUCSCFeatureDbTables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGFF' by 'txdbmaker::makeTxDbFromGFF' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromBiomart' by 'txdbmaker::makeTxDbPackageFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedMiRBaseBuildValues' by 'txdbmaker::supportedMiRBaseBuildValues' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTracks' by 'txdbmaker::supportedUCSCFeatureDbTracks' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::browseUCSCtrack' by 'txdbmaker::browseUCSCtrack' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::getChromInfoFromBiomart' by 'txdbmaker::getChromInfoFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGRanges' by 'txdbmaker::makeTxDbFromGRanges' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::supportedUCSCtables' by 'txdbmaker::supportedUCSCtables' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromBiomart' by 'txdbmaker::makeTxDbFromBiomart' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::UCSCFeatureDbTableSchema' by 'txdbmaker::UCSCFeatureDbTableSchema' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromEnsembl' by 'txdbmaker::makeTxDbFromEnsembl' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDb' by 'txdbmaker::makeTxDb' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFDbPackageFromUCSC' by 'txdbmaker::makeFDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbFromUCSC' by 'txdbmaker::makeTxDbFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromUCSC' by 'txdbmaker::makeTxDbPackageFromUCSC' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makePackageName' by 'txdbmaker::makePackageName' when loading 'customProDB' Warning: replacing previous import 'GenomicFeatures::makeFeatureDbFromUCSC' by 'txdbmaker::makeFeatureDbFromUCSC' when loading 'customProDB' ** testing if installed package keeps a record of temporary installation path * DONE (customProDB)
customProDB.Rcheck/customProDB-Ex.timings
name | user | system | elapsed | |
Bed2Range | 0.13 | 0.00 | 0.14 | |
InputVcf | 0.69 | 0.08 | 0.77 | |
JunctionType | 1.01 | 0.16 | 1.19 | |
Multiple_VCF | 0.86 | 0.04 | 0.90 | |
OutputNovelJun | 1.38 | 0.36 | 1.75 | |
OutputVarprocodingseq | 1.58 | 0.03 | 1.61 | |
OutputVarproseq | 0.59 | 0.00 | 0.59 | |
OutputVarproseq_single | 0.69 | 0.02 | 0.71 | |
Outputaberrant | 0.33 | 0.01 | 0.36 | |
Outputproseq | 0.52 | 0.04 | 0.54 | |
OutputsharedPro | 1.84 | 0.03 | 1.88 | |
Positionincoding | 0.34 | 0.03 | 0.38 | |
PrepareAnnotationEnsembl | 5.55 | 1.00 | 12.78 | |
PrepareAnnotationRefseq | 0 | 0 | 0 | |
SharedJunc | 0.57 | 0.00 | 0.57 | |
Varlocation | 0 | 0 | 0 | |
aaVariation | 0.57 | 0.03 | 0.60 | |
calculateRPKM | 0.56 | 0.03 | 0.59 | |
easyRun | 1.23 | 0.11 | 1.34 | |
easyRun_mul | 2.96 | 0.06 | 3.04 | |