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This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
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 1712/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.7.0  (landing page)
Qian Liu
Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: devel
git_last_commit: 85fc756
git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ReUseData on lconway

To the developers/maintainers of the ReUseData package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.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: ReUseData
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.7.0.tar.gz
StartedAt: 2024-11-28 01:29:59 -0500 (Thu, 28 Nov 2024)
EndedAt: 2024-11-28 01:35:36 -0500 (Thu, 28 Nov 2024)
EllapsedTime: 337.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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:
  .BBSoptions
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 ‘ReUseData’ 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
dataHub-class 5.515  0.709   6.335
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.


Installation output

ReUseData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘ReUseData’ ...
** 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 (ReUseData)

Tests output

ReUseData.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ReUseData)
> 
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
169fd4c6a4745_GRCh38.primary_assembly.genome.fa.1.bt2 added
169fd556d2a34_GRCh38.primary_assembly.genome.fa.2.bt2 added
169fd71ede7bc_GRCh38.primary_assembly.genome.fa.3.bt2 added
169fd3a092213_GRCh38.primary_assembly.genome.fa.4.bt2 added
169fd2d9c2b29_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
169fd67d5a823_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
169fd7c11c716_outfile.txt added
169fd7325b4fc_GRCh37_to_GRCh38.chain added
169fd308d4773_GRCh37_to_NCBI34.chain added
169fdb4de7ec_GRCh37_to_NCBI35.chain added
169fd27b53cc0_GRCh37_to_NCBI36.chain added
169fd6ba7759d_GRCh38_to_GRCh37.chain added
169fd3f1acda2_GRCh38_to_NCBI34.chain added
169fd78b2670b_GRCh38_to_NCBI35.chain added
169fd88b4115_GRCh38_to_NCBI36.chain added
169fd6e5dce14_NCBI34_to_GRCh37.chain added
169fd5084bba7_NCBI34_to_GRCh38.chain added
169fd3a3bfa3d_NCBI35_to_GRCh37.chain added
169fd37a9d8a9_NCBI35_to_GRCh38.chain added
169fd6fcf5bcb_NCBI36_to_GRCh37.chain added
169fd1693a5c6_NCBI36_to_GRCh38.chain added
169fd376875be_GRCm38_to_NCBIM36.chain added
169fd2b0a295d_GRCm38_to_NCBIM37.chain added
169fd2821aebe_NCBIM36_to_GRCm38.chain added
169fd3b575087_NCBIM37_to_GRCm38.chain added
169fd6167ed80_1000G_omni2.5.b37.vcf.gz added
169fd6e19a075_1000G_omni2.5.b37.vcf.gz.tbi added
169fd547599cb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
169fd74c409be_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
169fd725bd4d5_1000G_omni2.5.hg38.vcf.gz added
169fd6af2269a_1000G_omni2.5.hg38.vcf.gz.tbi added
169fd3fc47f50_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
169fd7d827de4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
169fd217441c_af-only-gnomad.raw.sites.vcf added
169fd45788b56_af-only-gnomad.raw.sites.vcf.idx added
169fd6d03debb_Mutect2-exome-panel.vcf.idx added
169fd1913fee7_Mutect2-WGS-panel-b37.vcf added
169fd6fc3fc8d_Mutect2-WGS-panel-b37.vcf.idx added
169fd2bf9c64e_small_exac_common_3.vcf added
169fd1b4a4170_small_exac_common_3.vcf.idx added
169fd280e2e0f_1000g_pon.hg38.vcf.gz added
169fd3af1ef54_1000g_pon.hg38.vcf.gz.tbi added
169fd61979207_af-only-gnomad.hg38.vcf.gz added
169fd25f43b9f_af-only-gnomad.hg38.vcf.gz.tbi added
169fd45765730_small_exac_common_3.hg38.vcf.gz added
169fd5c5633f0_small_exac_common_3.hg38.vcf.gz.tbi added
169fd1f6c00ec_gencode.v41.annotation.gtf added
169fd6bb09611_gencode.v42.annotation.gtf added
169fd164c6d53_gencode.vM30.annotation.gtf added
169fd739d6f94_gencode.vM31.annotation.gtf added
169fd650898d8_gencode.v41.transcripts.fa added
169fd176ac0ba_gencode.v41.transcripts.fa.fai added
169fd6192ff58_gencode.v42.transcripts.fa added
169fd79ba1c73_gencode.v42.transcripts.fa.fai added
169fd29a20074_gencode.vM30.pc_transcripts.fa added
169fd4acbd506_gencode.vM30.pc_transcripts.fa.fai added
169fdc0ea347_gencode.vM31.pc_transcripts.fa added
169fd15019080_gencode.vM31.pc_transcripts.fa.fai added
169fd19b5ce46_GRCh38.primary_assembly.genome.fa.1.ht2 added
169fd6ef962d9_GRCh38.primary_assembly.genome.fa.2.ht2 added
169fd36c8cd7a_GRCh38.primary_assembly.genome.fa.3.ht2 added
169fd392a20af_GRCh38.primary_assembly.genome.fa.4.ht2 added
169fd7cc7de7a_GRCh38.primary_assembly.genome.fa.5.ht2 added
169fd25df5b96_GRCh38.primary_assembly.genome.fa.6.ht2 added
169fd6af5e846_GRCh38.primary_assembly.genome.fa.7.ht2 added
169fd36648286_GRCh38.primary_assembly.genome.fa.8.ht2 added
169fdb54750_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
169fd7d5cd58c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
169fd59c81aa0_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
169fd604c2c6c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
169fd28f897d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
169fd58b8faeb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
169fd586187ce_GRCh38_full_analysis_set_plus_decoy_hla.fa added
169fd6b1b12b6_GRCh38.primary_assembly.genome.fa.fai added
169fd3e69a1a9_GRCh38.primary_assembly.genome.fa.amb added
169fd8f47e42_GRCh38.primary_assembly.genome.fa.ann added
169fd6b8d23a5_GRCh38.primary_assembly.genome.fa.bwt added
169fd7f1f5ccc_GRCh38.primary_assembly.genome.fa.pac added
169fd64059647_GRCh38.primary_assembly.genome.fa.sa added
169fd2acd429e_GRCh38.primary_assembly.genome.fa added
169fd9d0a906_hs37d5.fa.fai added
169fd6208cdf2_hs37d5.fa.amb added
169fd3008fd26_hs37d5.fa.ann added
169fd1e23e26d_hs37d5.fa.bwt added
169fd45e67190_hs37d5.fa.pac added
169fd1c29c8ca_hs37d5.fa.sa added
169fd7b3d5437_hs37d5.fa added
169fd77642616_complete_ref_lens.bin added
169fd5000ab96_ctable.bin added
169fd5c012de2_ctg_offsets.bin added
169fd516b7f9e_duplicate_clusters.tsv added
169fd688787d4_info.json added
169fd19e6a4e9_mphf.bin added
169fd7554ca47_pos.bin added
169fd11ac377f_pre_indexing.log added
169fd416f7be9_rank.bin added
169fd7e301f8e_ref_indexing.log added
169fd967e45b_refAccumLengths.bin added
169fd3c11730_reflengths.bin added
169fd79d9523c_refseq.bin added
169fd2aa61fa3_seq.bin added
169fd671c35_versionInfo.json added
169fd716cdbc7_salmon_index added
169fd21d11ffe_chrLength.txt added
169fd288b6e0a_chrName.txt added
169fd59e56751_chrNameLength.txt added
169fd63e224f2_chrStart.txt added
169fd13e7bf19_exonGeTrInfo.tab added
169fd53b30c84_exonInfo.tab added
169fdffad90a_geneInfo.tab added
169fd1dbf27b8_Genome added
169fd70c8b049_genomeParameters.txt added
169fd7adc278_Log.out added
169fd20ba5838_SA added
169fd29f5d551_SAindex added
169fd4a87ce5c_sjdbInfo.txt added
169fd19fd203e_sjdbList.fromGTF.out.tab added
169fd394fd3c6_sjdbList.out.tab added
169fd27d8898f_transcriptInfo.tab added
169fd792f1fb8_GRCh38.GENCODE.v42_100 added
169fd4cba730_knownGene_hg38.sql added
169fd564d42c5_knownGene_hg38.txt added
169fd6a5abfc6_refGene_hg38.sql added
169fd6be496b6_refGene_hg38.txt added
169fd6c62be10_knownGene_mm39.sql added
169fd46ac4407_knownGene_mm39.txt added
169fd57a64bd0_refGene_mm39.sql added
169fd66bb71a4_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes

Data is downloaded: 
/tmp/RtmpkGDuhU/test_gcpData/outfile.txt
}INFO Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added

Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.578   2.462  21.070 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class5.5150.7096.335
dataSearch0.9700.0441.020
dataUpdate000
getCloudData2.0450.1333.110
getData000
meta_data0.0010.0000.001
recipeHub-class0.1090.0100.120
recipeLoad1.0650.0721.145
recipeMake0.0000.0000.001
recipeSearch0.4540.0300.486
recipeUpdate000