Qian Liu
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 1745/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.4.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| 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: 2024-10-17 11:45:30 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 11:50:36 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 306.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.4.1 (2024-06-14)
* 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 ‘1.4.0’
* 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 13.146 1.354 16.587
getCloudData 4.979 0.226 6.426
* 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.
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)
ReUseData.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
ba61d5b50d9_GRCh38.primary_assembly.genome.fa.1.bt2 added
ba65618e59d_GRCh38.primary_assembly.genome.fa.2.bt2 added
ba67c8ad293_GRCh38.primary_assembly.genome.fa.3.bt2 added
ba67e06f0c5_GRCh38.primary_assembly.genome.fa.4.bt2 added
ba679a95626_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
ba65c571730_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
ba659b37fac_outfile.txt added
ba617832336_GRCh37_to_GRCh38.chain added
ba6227cba49_GRCh37_to_NCBI34.chain added
ba62aaa204f_GRCh37_to_NCBI35.chain added
ba672f386b_GRCh37_to_NCBI36.chain added
ba62d20fc7c_GRCh38_to_GRCh37.chain added
ba650a04809_GRCh38_to_NCBI34.chain added
ba64ad97039_GRCh38_to_NCBI35.chain added
ba6956d493_GRCh38_to_NCBI36.chain added
ba6239e03af_NCBI34_to_GRCh37.chain added
ba65b03e86d_NCBI34_to_GRCh38.chain added
ba65d907ac9_NCBI35_to_GRCh37.chain added
ba6386d521c_NCBI35_to_GRCh38.chain added
ba61129c935_NCBI36_to_GRCh37.chain added
ba64e58bf60_NCBI36_to_GRCh38.chain added
ba6247c5fcf_GRCm38_to_NCBIM36.chain added
ba6617621bf_GRCm38_to_NCBIM37.chain added
ba612a1b496_NCBIM36_to_GRCm38.chain added
ba63656ed68_NCBIM37_to_GRCm38.chain added
ba64fc62b7_1000G_omni2.5.b37.vcf.gz added
ba655b4deef_1000G_omni2.5.b37.vcf.gz.tbi added
ba6559848de_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
ba6d812b9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
ba669b5301d_1000G_omni2.5.hg38.vcf.gz added
ba67669f622_1000G_omni2.5.hg38.vcf.gz.tbi added
ba6269e6eea_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
ba66b83d874_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
ba61cf7ded1_af-only-gnomad.raw.sites.vcf added
ba655457a32_af-only-gnomad.raw.sites.vcf.idx added
ba64459945a_Mutect2-exome-panel.vcf.idx added
ba6551ac3c4_Mutect2-WGS-panel-b37.vcf added
ba6502aa482_Mutect2-WGS-panel-b37.vcf.idx added
ba61f967bec_small_exac_common_3.vcf added
ba650a1d327_small_exac_common_3.vcf.idx added
ba6302dcecc_1000g_pon.hg38.vcf.gz added
ba6f63cbca_1000g_pon.hg38.vcf.gz.tbi added
ba660d842aa_af-only-gnomad.hg38.vcf.gz added
ba61600d892_af-only-gnomad.hg38.vcf.gz.tbi added
ba6118a6487_small_exac_common_3.hg38.vcf.gz added
ba614cde410_small_exac_common_3.hg38.vcf.gz.tbi added
ba65937e11b_gencode.v41.annotation.gtf added
ba6639be15f_gencode.v42.annotation.gtf added
ba6ee95710_gencode.vM30.annotation.gtf added
ba67952e315_gencode.vM31.annotation.gtf added
ba630bab5ed_gencode.v41.transcripts.fa added
ba631fdf399_gencode.v41.transcripts.fa.fai added
ba61783db73_gencode.v42.transcripts.fa added
ba651bc6714_gencode.v42.transcripts.fa.fai added
ba628137bf8_gencode.vM30.pc_transcripts.fa added
ba6172feb56_gencode.vM30.pc_transcripts.fa.fai added
ba64b0366fe_gencode.vM31.pc_transcripts.fa added
ba64c5ed42b_gencode.vM31.pc_transcripts.fa.fai added
ba665bb7a38_GRCh38.primary_assembly.genome.fa.1.ht2 added
ba6775526b5_GRCh38.primary_assembly.genome.fa.2.ht2 added
ba677607247_GRCh38.primary_assembly.genome.fa.3.ht2 added
ba65ceed08b_GRCh38.primary_assembly.genome.fa.4.ht2 added
ba642bd8557_GRCh38.primary_assembly.genome.fa.5.ht2 added
ba6287d34fc_GRCh38.primary_assembly.genome.fa.6.ht2 added
ba63421a128_GRCh38.primary_assembly.genome.fa.7.ht2 added
ba6bdb63d5_GRCh38.primary_assembly.genome.fa.8.ht2 added
ba670773b07_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
ba623c48240_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
ba63a434a18_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
ba617b58b8a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
ba6fdc1d2f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
ba63c0000cb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
ba624342e33_GRCh38_full_analysis_set_plus_decoy_hla.fa added
ba65dc528d6_GRCh38.primary_assembly.genome.fa.fai added
ba63afc29b2_GRCh38.primary_assembly.genome.fa.amb added
ba6115835f_GRCh38.primary_assembly.genome.fa.ann added
ba62b63d287_GRCh38.primary_assembly.genome.fa.bwt added
ba62692b352_GRCh38.primary_assembly.genome.fa.pac added
ba6693ae046_GRCh38.primary_assembly.genome.fa.sa added
ba6185a49a3_GRCh38.primary_assembly.genome.fa added
ba64f9878d2_hs37d5.fa.fai added
ba623244bd1_hs37d5.fa.amb added
ba623ed985d_hs37d5.fa.ann added
ba643ae1418_hs37d5.fa.bwt added
ba659a9565e_hs37d5.fa.pac added
ba67c65634e_hs37d5.fa.sa added
ba6645ad5af_hs37d5.fa added
ba678307a2_complete_ref_lens.bin added
ba62b6a2088_ctable.bin added
ba6447dd6fc_ctg_offsets.bin added
ba621ad5d85_duplicate_clusters.tsv added
ba67cd6d808_info.json added
ba67d01353f_mphf.bin added
ba65a4efb36_pos.bin added
ba6774ec48b_pre_indexing.log added
ba65449bede_rank.bin added
ba635920c0d_ref_indexing.log added
ba675544f5_refAccumLengths.bin added
ba66f223495_reflengths.bin added
ba62eaa5b33_refseq.bin added
ba632498934_seq.bin added
ba679ceceb6_versionInfo.json added
ba678654d33_salmon_index added
ba642af8d05_chrLength.txt added
ba613536577_chrName.txt added
ba6482a718a_chrNameLength.txt added
ba65a844009_chrStart.txt added
ba620883d4c_exonGeTrInfo.tab added
ba650705943_exonInfo.tab added
ba67ff466f6_geneInfo.tab added
ba6693e21b_Genome added
ba656e15dfc_genomeParameters.txt added
ba665e177f3_Log.out added
ba6358a26c6_SA added
ba6f7aca0_SAindex added
ba64663cdf_sjdbInfo.txt added
ba6542656ba_sjdbList.fromGTF.out.tab added
ba62107f87f_sjdbList.out.tab added
ba6124b6aca_transcriptInfo.tab added
ba6154ffd28_GRCh38.GENCODE.v42_100 added
ba636755806_knownGene_hg38.sql added
ba651e60dd8_knownGene_hg38.txt added
ba6569709e9_refGene_hg38.sql added
ba6560bcc68_refGene_hg38.txt added
ba62098ebfa_knownGene_mm39.sql added
ba617ac7ace_knownGene_mm39.txt added
ba63cb27686_refGene_mm39.sql added
ba66883768b_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/RtmpfRx7gH/test_gcpData/outfile.txt
}[1;30mINFO[0m 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
44.157 5.280 58.929
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 13.146 | 1.354 | 16.587 | |
| dataSearch | 2.745 | 0.090 | 3.116 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 4.979 | 0.226 | 6.426 | |
| getData | 0.000 | 0.001 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.289 | 0.018 | 0.321 | |
| recipeLoad | 2.980 | 0.148 | 3.555 | |
| recipeMake | 0.000 | 0.001 | 0.002 | |
| recipeSearch | 1.193 | 0.057 | 1.442 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |