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This page was generated on 2024-05-04 11:39:50 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1745/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.4.0  (landing page)
Qian Liu
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: RELEASE_3_19
git_last_commit: 801f620
git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2024-05-04 00:22:38 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:25:30 -0400 (Sat, 04 May 2024)
EllapsedTime: 172.1 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.4.0’
* package encoding: UTF-8
* 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:
  .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 8.430  1.003   9.591
getCloudData  3.105  0.182  10.041
* 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-3.19-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/4.4-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 version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
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...
117af88cf9c7_GRCh38.primary_assembly.genome.fa.1.bt2 added
117af5f627c33_GRCh38.primary_assembly.genome.fa.2.bt2 added
117af3ac82931_GRCh38.primary_assembly.genome.fa.3.bt2 added
117af2b086e1d_GRCh38.primary_assembly.genome.fa.4.bt2 added
117af367547fd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
117af4dc94ef9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
117af5b5fe554_outfile.txt added
117af74c91ca9_GRCh37_to_GRCh38.chain added
117af3f78d725_GRCh37_to_NCBI34.chain added
117af1674deb1_GRCh37_to_NCBI35.chain added
117af52c841fb_GRCh37_to_NCBI36.chain added
117af5963f032_GRCh38_to_GRCh37.chain added
117af302e9077_GRCh38_to_NCBI34.chain added
117af410e8d57_GRCh38_to_NCBI35.chain added
117af22616c1f_GRCh38_to_NCBI36.chain added
117af2a0178db_NCBI34_to_GRCh37.chain added
117af46a58768_NCBI34_to_GRCh38.chain added
117af1d5ce114_NCBI35_to_GRCh37.chain added
117af3cbcf71b_NCBI35_to_GRCh38.chain added
117af1a032cc4_NCBI36_to_GRCh37.chain added
117af46700533_NCBI36_to_GRCh38.chain added
117af64657b65_GRCm38_to_NCBIM36.chain added
117af42885761_GRCm38_to_NCBIM37.chain added
117af520c367_NCBIM36_to_GRCm38.chain added
117af29fca1d2_NCBIM37_to_GRCm38.chain added
117af8e3f787_1000G_omni2.5.b37.vcf.gz added
117af2e8fc4a0_1000G_omni2.5.b37.vcf.gz.tbi added
117af60b5fc41_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
117af4bc44101_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
117af4187cf83_1000G_omni2.5.hg38.vcf.gz added
117af3b48c311_1000G_omni2.5.hg38.vcf.gz.tbi added
117af25feaf7f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
117af73b3ce55_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
117af21af69cb_af-only-gnomad.raw.sites.vcf added
117af34a9fb4_af-only-gnomad.raw.sites.vcf.idx added
117af183ae41c_Mutect2-exome-panel.vcf.idx added
117af4255f6b1_Mutect2-WGS-panel-b37.vcf added
117af19b7007d_Mutect2-WGS-panel-b37.vcf.idx added
117af3d811bbb_small_exac_common_3.vcf added
117af6743b188_small_exac_common_3.vcf.idx added
117afd3c8caf_1000g_pon.hg38.vcf.gz added
117af2383bf3_1000g_pon.hg38.vcf.gz.tbi added
117af39e7cfa8_af-only-gnomad.hg38.vcf.gz added
117af21f23c4b_af-only-gnomad.hg38.vcf.gz.tbi added
117af26547156_small_exac_common_3.hg38.vcf.gz added
117af71dcd8c2_small_exac_common_3.hg38.vcf.gz.tbi added
117af5a1ae2f4_gencode.v41.annotation.gtf added
117af1b2a2f63_gencode.v42.annotation.gtf added
117af6e8d1a83_gencode.vM30.annotation.gtf added
117af71c7c728_gencode.vM31.annotation.gtf added
117af72e44d73_gencode.v41.transcripts.fa added
117af6a98f3f2_gencode.v41.transcripts.fa.fai added
117af5fb7cb8a_gencode.v42.transcripts.fa added
117af1b94021e_gencode.v42.transcripts.fa.fai added
117af12170db7_gencode.vM30.pc_transcripts.fa added
117af278572a8_gencode.vM30.pc_transcripts.fa.fai added
117af2a2a87dd_gencode.vM31.pc_transcripts.fa added
117af4e3dd3cb_gencode.vM31.pc_transcripts.fa.fai added
117af3d1bdc8e_GRCh38.primary_assembly.genome.fa.1.ht2 added
117af702d0df9_GRCh38.primary_assembly.genome.fa.2.ht2 added
117af1df08ff8_GRCh38.primary_assembly.genome.fa.3.ht2 added
117af1c7bf223_GRCh38.primary_assembly.genome.fa.4.ht2 added
117afd55e671_GRCh38.primary_assembly.genome.fa.5.ht2 added
117af28c0b8e_GRCh38.primary_assembly.genome.fa.6.ht2 added
117af384a98f0_GRCh38.primary_assembly.genome.fa.7.ht2 added
117af297ed16f_GRCh38.primary_assembly.genome.fa.8.ht2 added
117af44e7e3b1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
117af54159cce_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
117af56e9c382_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
117afd22b862_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
117af627730aa_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
117af7f1c1b66_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
117afe4b06bc_GRCh38_full_analysis_set_plus_decoy_hla.fa added
117af5fa727f8_GRCh38.primary_assembly.genome.fa.fai added
117af57313bd7_GRCh38.primary_assembly.genome.fa.amb added
117af614fccf9_GRCh38.primary_assembly.genome.fa.ann added
117af3e1a2158_GRCh38.primary_assembly.genome.fa.bwt added
117af25833842_GRCh38.primary_assembly.genome.fa.pac added
117af49e2884b_GRCh38.primary_assembly.genome.fa.sa added
117af376219d2_GRCh38.primary_assembly.genome.fa added
117af98d4666_hs37d5.fa.fai added
117af1a08d770_hs37d5.fa.amb added
117af3a78076a_hs37d5.fa.ann added
117af1e2ede23_hs37d5.fa.bwt added
117af16f9db50_hs37d5.fa.pac added
117af6dad6cf8_hs37d5.fa.sa added
117af14cd4609_hs37d5.fa added
117af30b1038a_complete_ref_lens.bin added
117af355f71ff_ctable.bin added
117afd3537b9_ctg_offsets.bin added
117af20dd5975_duplicate_clusters.tsv added
117af241c212e_info.json added
117af32c66587_mphf.bin added
117af7f339c1b_pos.bin added
117af154df1db_pre_indexing.log added
117af30416bca_rank.bin added
117af170bb386_ref_indexing.log added
117af1372e3c_refAccumLengths.bin added
117af4dbc65c3_reflengths.bin added
117afbbd0d14_refseq.bin added
117af28a5a211_seq.bin added
117af12331ef0_versionInfo.json added
117af5a3427e5_salmon_index added
117af162759a7_chrLength.txt added
117af716eee4d_chrName.txt added
117af29df3b69_chrNameLength.txt added
117af7eb57ff8_chrStart.txt added
117af3de4b3c5_exonGeTrInfo.tab added
117af71d66a41_exonInfo.tab added
117af33da0bca_geneInfo.tab added
117af303c155e_Genome added
117af389ee70f_genomeParameters.txt added
117af4853a6d3_Log.out added
117af6bed8bbd_SA added
117af38715ca6_SAindex added
117af1a79b33d_sjdbInfo.txt added
117af2be6775f_sjdbList.fromGTF.out.tab added
117af27a7147d_sjdbList.out.tab added
117af4a322ee1_transcriptInfo.tab added
117af24a3dbd5_GRCh38.GENCODE.v42_100 added
117af1b58fbe_knownGene_hg38.sql added
117af36f003d2_knownGene_hg38.txt added
117af478aec2b_refGene_hg38.sql added
117af71971fbe_refGene_hg38.txt added
117af78a52d34_knownGene_mm39.sql added
117af243aeecd_knownGene_mm39.txt added
117af1913e750_refGene_mm39.sql added
117af69b7420c_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/Rtmpgbc9c4/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 
 26.618   3.724  32.020 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class8.4301.0039.591
dataSearch1.5540.0731.646
dataUpdate000
getCloudData 3.105 0.18210.041
getData0.0000.0010.001
meta_data0.0010.0000.001
recipeHub-class0.1660.0150.185
recipeLoad1.7130.1131.848
recipeMake0.0010.0010.001
recipeSearch0.7250.0480.781
recipeUpdate0.0000.0010.001