Qian Liu
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 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) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1714/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.7.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.7.0 |
| 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: 2024-12-23 22:38:55 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 22:41:26 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 151.4 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_1.7.0.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 ... 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 7.698 0.920 8.753
getCloudData 2.745 0.156 6.631
* 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.
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)
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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
ff372c2b14ef_GRCh38.primary_assembly.genome.fa.1.bt2 added
ff37406b6d90_GRCh38.primary_assembly.genome.fa.2.bt2 added
ff374ce629fa_GRCh38.primary_assembly.genome.fa.3.bt2 added
ff371ace0387_GRCh38.primary_assembly.genome.fa.4.bt2 added
ff374b49a1d0_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
ff374f1e854d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
ff375cc1aacf_outfile.txt added
ff372eb52b9c_GRCh37_to_GRCh38.chain added
ff37784226b8_GRCh37_to_NCBI34.chain added
ff373efc37b6_GRCh37_to_NCBI35.chain added
ff3720adae08_GRCh37_to_NCBI36.chain added
ff376a7c9ffa_GRCh38_to_GRCh37.chain added
ff371beb0cb4_GRCh38_to_NCBI34.chain added
ff37648f0bbd_GRCh38_to_NCBI35.chain added
ff376b4bd8de_GRCh38_to_NCBI36.chain added
ff37408b0dda_NCBI34_to_GRCh37.chain added
ff37693a8450_NCBI34_to_GRCh38.chain added
ff37c4d629_NCBI35_to_GRCh37.chain added
ff377ac81e23_NCBI35_to_GRCh38.chain added
ff376832cace_NCBI36_to_GRCh37.chain added
ff375ea0cfd3_NCBI36_to_GRCh38.chain added
ff37fac562e_GRCm38_to_NCBIM36.chain added
ff377b4dee0b_GRCm38_to_NCBIM37.chain added
ff373947536b_NCBIM36_to_GRCm38.chain added
ff3779b5b32d_NCBIM37_to_GRCm38.chain added
ff378068dc8_1000G_omni2.5.b37.vcf.gz added
ff3766464995_1000G_omni2.5.b37.vcf.gz.tbi added
ff37108909a8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
ff3714d8fd13_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
ff3731cef516_1000G_omni2.5.hg38.vcf.gz added
ff37a3c90e6_1000G_omni2.5.hg38.vcf.gz.tbi added
ff37e4cf14a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
ff375d75389b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
ff373ad7780c_af-only-gnomad.raw.sites.vcf added
ff37180a7a02_af-only-gnomad.raw.sites.vcf.idx added
ff3757d025a2_Mutect2-exome-panel.vcf.idx added
ff372256dbb8_Mutect2-WGS-panel-b37.vcf added
ff3774731ea4_Mutect2-WGS-panel-b37.vcf.idx added
ff3731e0dcb6_small_exac_common_3.vcf added
ff3721ba4a4f_small_exac_common_3.vcf.idx added
ff374d6499d5_1000g_pon.hg38.vcf.gz added
ff377af96a5_1000g_pon.hg38.vcf.gz.tbi added
ff3718cb2e94_af-only-gnomad.hg38.vcf.gz added
ff37435f0343_af-only-gnomad.hg38.vcf.gz.tbi added
ff3712cf4643_small_exac_common_3.hg38.vcf.gz added
ff37660de25a_small_exac_common_3.hg38.vcf.gz.tbi added
ff371987b70e_gencode.v41.annotation.gtf added
ff371d03053a_gencode.v42.annotation.gtf added
ff37314c31b7_gencode.vM30.annotation.gtf added
ff37153feaa_gencode.vM31.annotation.gtf added
ff3731744b94_gencode.v41.transcripts.fa added
ff374a0dfae9_gencode.v41.transcripts.fa.fai added
ff375bd3fcfa_gencode.v42.transcripts.fa added
ff373a85b02f_gencode.v42.transcripts.fa.fai added
ff371ef1fbad_gencode.vM30.pc_transcripts.fa added
ff3720c22aba_gencode.vM30.pc_transcripts.fa.fai added
ff372b832a23_gencode.vM31.pc_transcripts.fa added
ff3730437626_gencode.vM31.pc_transcripts.fa.fai added
ff371d01d18b_GRCh38.primary_assembly.genome.fa.1.ht2 added
ff3762640b8d_GRCh38.primary_assembly.genome.fa.2.ht2 added
ff3716328872_GRCh38.primary_assembly.genome.fa.3.ht2 added
ff374f9bffc0_GRCh38.primary_assembly.genome.fa.4.ht2 added
ff37ab3bf15_GRCh38.primary_assembly.genome.fa.5.ht2 added
ff371ec60130_GRCh38.primary_assembly.genome.fa.6.ht2 added
ff3759780618_GRCh38.primary_assembly.genome.fa.7.ht2 added
ff3756d83f8b_GRCh38.primary_assembly.genome.fa.8.ht2 added
ff37f33eb38_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
ff371997b154_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
ff3735fb0eec_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
ff377590c3a3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
ff37731c3ea1_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
ff374353f711_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
ff373d819f9f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
ff379169f45_GRCh38.primary_assembly.genome.fa.fai added
ff372c326fac_GRCh38.primary_assembly.genome.fa.amb added
ff3723419bdf_GRCh38.primary_assembly.genome.fa.ann added
ff3728605f8e_GRCh38.primary_assembly.genome.fa.bwt added
ff374f217857_GRCh38.primary_assembly.genome.fa.pac added
ff371e63c057_GRCh38.primary_assembly.genome.fa.sa added
ff3726e89f57_GRCh38.primary_assembly.genome.fa added
ff3772351cb5_hs37d5.fa.fai added
ff377cefe9a6_hs37d5.fa.amb added
ff376ad4d15e_hs37d5.fa.ann added
ff3739fda91d_hs37d5.fa.bwt added
ff373c69cca9_hs37d5.fa.pac added
ff3745fb8a3b_hs37d5.fa.sa added
ff375304b62_hs37d5.fa added
ff3725a51197_complete_ref_lens.bin added
ff377825e3cf_ctable.bin added
ff377f8f68a8_ctg_offsets.bin added
ff3720202f05_duplicate_clusters.tsv added
ff3720ef01bd_info.json added
ff372b5b302f_mphf.bin added
ff376fb873e5_pos.bin added
ff3736c0f8b0_pre_indexing.log added
ff37370706e5_rank.bin added
ff372e55c09c_ref_indexing.log added
ff377fd85987_refAccumLengths.bin added
ff3754ddefa3_reflengths.bin added
ff37369fe1dc_refseq.bin added
ff373aa54e88_seq.bin added
ff373ac6e0cc_versionInfo.json added
ff3756d08f39_salmon_index added
ff37166b13b6_chrLength.txt added
ff374fdb1d39_chrName.txt added
ff373a5bb224_chrNameLength.txt added
ff375a0c776a_chrStart.txt added
ff376873fe55_exonGeTrInfo.tab added
ff37173eb406_exonInfo.tab added
ff37159d01d6_geneInfo.tab added
ff3776e393af_Genome added
ff3756f50323_genomeParameters.txt added
ff376fa11b6e_Log.out added
ff373a100c03_SA added
ff377384b6bc_SAindex added
ff37df92be4_sjdbInfo.txt added
ff3761b08ce6_sjdbList.fromGTF.out.tab added
ff37df28225_sjdbList.out.tab added
ff372c3e524a_transcriptInfo.tab added
ff372f8c8ef7_GRCh38.GENCODE.v42_100 added
ff3734fe1284_knownGene_hg38.sql added
ff371471b34a_knownGene_hg38.txt added
ff3734b1c9c2_refGene_hg38.sql added
ff37434fa95_refGene_hg38.txt added
ff37322f4e5b_knownGene_mm39.sql added
ff373fc1521a_knownGene_mm39.txt added
ff372cf549a9_refGene_mm39.sql added
ff371bb70d4e_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/RtmpaQ0T7q/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
22.984 2.908 26.897
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.698 | 0.920 | 8.753 | |
| dataSearch | 1.563 | 0.080 | 1.681 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.745 | 0.156 | 6.631 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.149 | 0.014 | 0.163 | |
| recipeLoad | 1.539 | 0.104 | 1.661 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.685 | 0.044 | 0.734 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |