Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 480/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.46.0  (landing page)
Xiaojing Wang
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/customProDB
git_branch: RELEASE_3_20
git_last_commit: 585e069
git_last_commit_date: 2024-10-29 09:46:25 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for customProDB on teran2

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.

raw results


Summary

Package: customProDB
Version: 1.46.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings customProDB_1.46.0.tar.gz
StartedAt: 2024-11-20 01:14:00 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 01:19:14 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 314.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: customProDB.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings customProDB_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.46.0’
* 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 ... 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 ‘/media/volume/teran2_disk/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 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
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 4.036  0.121  12.351
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck/00check.log’
for details.


Installation output

customProDB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL customProDB
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output


Example timings

customProDB.Rcheck/customProDB-Ex.timings

nameusersystemelapsed
Bed2Range0.0590.0180.111
InputVcf1.6770.0772.122
JunctionType0.5130.1270.728
Multiple_VCF0.4630.1320.627
OutputNovelJun0.9510.0842.457
OutputVarprocodingseq0.3770.0220.489
OutputVarproseq0.3380.0130.356
OutputVarproseq_single0.3440.0150.442
Outputaberrant0.1810.0130.207
Outputproseq0.3960.0040.424
OutputsharedPro1.1390.0121.252
Positionincoding0.2520.0060.337
PrepareAnnotationEnsembl 4.036 0.12112.351
PrepareAnnotationRefseq0.0000.0000.001
SharedJunc0.4050.0250.625
Varlocation000
aaVariation0.3590.0170.508
calculateRPKM0.3840.0060.454
easyRun0.8330.0200.983
easyRun_mul1.9500.0222.124