Qian Liu
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: cbe4e73 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -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 1693/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.4 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-06-10 08:45:48 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 08:50:47 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 299.4 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.5.0’
* 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 13.335 1.298 16.737
getCloudData 5.038 0.207 6.621
* 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-3.20-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 4.4.0 Patched (2024-04-24 r86482) -- "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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
11b675e6085e8_GRCh38.primary_assembly.genome.fa.1.bt2 added
11b6712f772c0_GRCh38.primary_assembly.genome.fa.2.bt2 added
11b67338ea4fa_GRCh38.primary_assembly.genome.fa.3.bt2 added
11b6759f13387_GRCh38.primary_assembly.genome.fa.4.bt2 added
11b676a6e1232_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
11b67606cc734_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
11b6758a5861_outfile.txt added
11b673db04b1e_GRCh37_to_GRCh38.chain added
11b67113be36_GRCh37_to_NCBI34.chain added
11b67372ccbc7_GRCh37_to_NCBI35.chain added
11b675df6921d_GRCh37_to_NCBI36.chain added
11b6766f2de1c_GRCh38_to_GRCh37.chain added
11b6752d43511_GRCh38_to_NCBI34.chain added
11b6769e81992_GRCh38_to_NCBI35.chain added
11b674e6f690_GRCh38_to_NCBI36.chain added
11b6757456a73_NCBI34_to_GRCh37.chain added
11b67e4fd0c8_NCBI34_to_GRCh38.chain added
11b671a1401cf_NCBI35_to_GRCh37.chain added
11b671782ca69_NCBI35_to_GRCh38.chain added
11b67bb6bf8e_NCBI36_to_GRCh37.chain added
11b67ada09a4_NCBI36_to_GRCh38.chain added
11b6770aef38c_GRCm38_to_NCBIM36.chain added
11b676df7a61f_GRCm38_to_NCBIM37.chain added
11b671dbb75a0_NCBIM36_to_GRCm38.chain added
11b677e276a9f_NCBIM37_to_GRCm38.chain added
11b674dc92d6d_1000G_omni2.5.b37.vcf.gz added
11b6752c57700_1000G_omni2.5.b37.vcf.gz.tbi added
11b672207cb74_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
11b672dbe3e20_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
11b6724e0be56_1000G_omni2.5.hg38.vcf.gz added
11b671ef01304_1000G_omni2.5.hg38.vcf.gz.tbi added
11b6723707b7a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
11b672dba98c3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
11b67358341a9_af-only-gnomad.raw.sites.vcf added
11b673c4bd9b1_af-only-gnomad.raw.sites.vcf.idx added
11b6717c11264_Mutect2-exome-panel.vcf.idx added
11b6749e6f6b_Mutect2-WGS-panel-b37.vcf added
11b673da4dc2b_Mutect2-WGS-panel-b37.vcf.idx added
11b671272aaab_small_exac_common_3.vcf added
11b672622ca03_small_exac_common_3.vcf.idx added
11b6735fc9e84_1000g_pon.hg38.vcf.gz added
11b675c0b07cc_1000g_pon.hg38.vcf.gz.tbi added
11b67582d1149_af-only-gnomad.hg38.vcf.gz added
11b6776c9fcd8_af-only-gnomad.hg38.vcf.gz.tbi added
11b6746f705d5_small_exac_common_3.hg38.vcf.gz added
11b673a00759_small_exac_common_3.hg38.vcf.gz.tbi added
11b677f4265ea_gencode.v41.annotation.gtf added
11b67603126eb_gencode.v42.annotation.gtf added
11b673af23fa3_gencode.vM30.annotation.gtf added
11b6776300490_gencode.vM31.annotation.gtf added
11b674a7bc68e_gencode.v41.transcripts.fa added
11b67428bad6_gencode.v41.transcripts.fa.fai added
11b67e0239bc_gencode.v42.transcripts.fa added
11b67341c6cd3_gencode.v42.transcripts.fa.fai added
11b67362cab5f_gencode.vM30.pc_transcripts.fa added
11b672ea705c2_gencode.vM30.pc_transcripts.fa.fai added
11b67576b1b7b_gencode.vM31.pc_transcripts.fa added
11b6738d95513_gencode.vM31.pc_transcripts.fa.fai added
11b6744606f8d_GRCh38.primary_assembly.genome.fa.1.ht2 added
11b67173bb50d_GRCh38.primary_assembly.genome.fa.2.ht2 added
11b6750eb7465_GRCh38.primary_assembly.genome.fa.3.ht2 added
11b671226bc64_GRCh38.primary_assembly.genome.fa.4.ht2 added
11b672d1a528b_GRCh38.primary_assembly.genome.fa.5.ht2 added
11b671b213acf_GRCh38.primary_assembly.genome.fa.6.ht2 added
11b67229bf9f3_GRCh38.primary_assembly.genome.fa.7.ht2 added
11b672e36d245_GRCh38.primary_assembly.genome.fa.8.ht2 added
11b671126c7b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
11b67901c82d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
11b6753fd06f9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
11b678d4f083_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
11b6753fa2cfc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
11b674d9f7f76_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
11b67226943ca_GRCh38_full_analysis_set_plus_decoy_hla.fa added
11b672ce1946c_GRCh38.primary_assembly.genome.fa.fai added
11b67dd75579_GRCh38.primary_assembly.genome.fa.amb added
11b67342c8208_GRCh38.primary_assembly.genome.fa.ann added
11b67560cf5fa_GRCh38.primary_assembly.genome.fa.bwt added
11b676ce91c38_GRCh38.primary_assembly.genome.fa.pac added
11b673c3bd864_GRCh38.primary_assembly.genome.fa.sa added
11b677cfbac20_GRCh38.primary_assembly.genome.fa added
11b676ee1a8fa_hs37d5.fa.fai added
11b67211cedf5_hs37d5.fa.amb added
11b67724a80ce_hs37d5.fa.ann added
11b67794e8f00_hs37d5.fa.bwt added
11b67148e8738_hs37d5.fa.pac added
11b67194f7813_hs37d5.fa.sa added
11b6730543460_hs37d5.fa added
11b67683aa369_complete_ref_lens.bin added
11b6761be77f4_ctable.bin added
11b671fb5664e_ctg_offsets.bin added
11b673e4f9b25_duplicate_clusters.tsv added
11b675c52ba18_info.json added
11b673b37ad02_mphf.bin added
11b67443f7cad_pos.bin added
11b67241264dc_pre_indexing.log added
11b67339bba04_rank.bin added
11b6734d17714_ref_indexing.log added
11b6723e0dd23_refAccumLengths.bin added
11b677fd6373b_reflengths.bin added
11b6748c4440e_refseq.bin added
11b674d501874_seq.bin added
11b6745758f53_versionInfo.json added
11b672914b5c5_salmon_index added
11b67ea9ad95_chrLength.txt added
11b6725c318b8_chrName.txt added
11b672b8beb66_chrNameLength.txt added
11b676f0b8bdf_chrStart.txt added
11b675f0c166d_exonGeTrInfo.tab added
11b6712947edb_exonInfo.tab added
11b6753146564_geneInfo.tab added
11b67600cb2d8_Genome added
11b6761b1b42b_genomeParameters.txt added
11b6759aba528_Log.out added
11b6713e81316_SA added
11b67693d138f_SAindex added
11b6728cf4743_sjdbInfo.txt added
11b67404f94a3_sjdbList.fromGTF.out.tab added
11b6728a77a51_sjdbList.out.tab added
11b67b4f70b1_transcriptInfo.tab added
11b67c6f7a44_GRCh38.GENCODE.v42_100 added
11b676ac40cbc_knownGene_hg38.sql added
11b676d204166_knownGene_hg38.txt added
11b6760a5c782_refGene_hg38.sql added
11b6723cd5960_refGene_hg38.txt added
11b677ea6bffc_knownGene_mm39.sql added
11b6775867a59_knownGene_mm39.txt added
11b674fcaa556_refGene_mm39.sql added
11b6712cda07_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/RtmpmG2HnW/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
45.476 5.203 55.464
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 13.335 | 1.298 | 16.737 | |
| dataSearch | 2.694 | 0.082 | 3.095 | |
| dataUpdate | 0.000 | 0.001 | 0.003 | |
| getCloudData | 5.038 | 0.207 | 6.621 | |
| getData | 0.001 | 0.001 | 0.002 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.302 | 0.020 | 0.335 | |
| recipeLoad | 3.051 | 0.142 | 3.386 | |
| recipeMake | 0.001 | 0.001 | 0.002 | |
| recipeSearch | 1.354 | 0.059 | 1.480 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |