Qian Liu
| Snapshot Date: 2024-09-26 13:40 -0400 (Thu, 26 Sep 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 2024-09-27 12:30 -0400 (Fri, 27 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4451 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
| 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 1708/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (landing page) Qian Liu
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 1.5.0 |
| 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: 2024-09-26 23:16:08 -0400 (Thu, 26 Sep 2024) |
| EndedAt: 2024-09-26 23:18:45 -0400 (Thu, 26 Sep 2024) |
| EllapsedTime: 156.9 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 4.4.1 (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 12.7.1
* 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 7.94 0.941 9.029
* 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 4.4.1 (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...
145b3773345d_GRCh38.primary_assembly.genome.fa.1.bt2 added
145b6c72e21b_GRCh38.primary_assembly.genome.fa.2.bt2 added
145b6a5a923c_GRCh38.primary_assembly.genome.fa.3.bt2 added
145b6036d7b0_GRCh38.primary_assembly.genome.fa.4.bt2 added
145b308a9529_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
145b5a46cfa4_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
145b5eea4649_outfile.txt added
145b66ac934d_GRCh37_to_GRCh38.chain added
145b4bfad8e4_GRCh37_to_NCBI34.chain added
145b41b587b4_GRCh37_to_NCBI35.chain added
145b74e05c1f_GRCh37_to_NCBI36.chain added
145b35c0332b_GRCh38_to_GRCh37.chain added
145b5d5f679e_GRCh38_to_NCBI34.chain added
145b228be5f6_GRCh38_to_NCBI35.chain added
145bea68b32_GRCh38_to_NCBI36.chain added
145b57fc8721_NCBI34_to_GRCh37.chain added
145b40bb4a8_NCBI34_to_GRCh38.chain added
145b1c8183ab_NCBI35_to_GRCh37.chain added
145b7aeb5e2b_NCBI35_to_GRCh38.chain added
145b72739818_NCBI36_to_GRCh37.chain added
145b3068a5c_NCBI36_to_GRCh38.chain added
145b22659f91_GRCm38_to_NCBIM36.chain added
145b3dcefa3b_GRCm38_to_NCBIM37.chain added
145b5f8e5730_NCBIM36_to_GRCm38.chain added
145b79fe4152_NCBIM37_to_GRCm38.chain added
145b2372ad10_1000G_omni2.5.b37.vcf.gz added
145b3dc0079e_1000G_omni2.5.b37.vcf.gz.tbi added
145ba3435be_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
145b69b4522d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
145b3d7f3e92_1000G_omni2.5.hg38.vcf.gz added
145b6ce502c8_1000G_omni2.5.hg38.vcf.gz.tbi added
145b2f19d052_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
145b47bbcfa6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
145b7b3dc014_af-only-gnomad.raw.sites.vcf added
145b130da042_af-only-gnomad.raw.sites.vcf.idx added
145b639456d3_Mutect2-exome-panel.vcf.idx added
145b1fd069b8_Mutect2-WGS-panel-b37.vcf added
145b2bccbf59_Mutect2-WGS-panel-b37.vcf.idx added
145bf268286_small_exac_common_3.vcf added
145b2943332f_small_exac_common_3.vcf.idx added
145b7ad567d2_1000g_pon.hg38.vcf.gz added
145b50934afe_1000g_pon.hg38.vcf.gz.tbi added
145b76209305_af-only-gnomad.hg38.vcf.gz added
145b549469d9_af-only-gnomad.hg38.vcf.gz.tbi added
145b5bb150f0_small_exac_common_3.hg38.vcf.gz added
145b5638eb97_small_exac_common_3.hg38.vcf.gz.tbi added
145b32f332ba_gencode.v41.annotation.gtf added
145b7c876b77_gencode.v42.annotation.gtf added
145b1ea09180_gencode.vM30.annotation.gtf added
145b3fb07a35_gencode.vM31.annotation.gtf added
145b5b274e3d_gencode.v41.transcripts.fa added
145b7181b58b_gencode.v41.transcripts.fa.fai added
145b7ab5f2e4_gencode.v42.transcripts.fa added
145b3f5d95ac_gencode.v42.transcripts.fa.fai added
145b190d6fb4_gencode.vM30.pc_transcripts.fa added
145b41209f45_gencode.vM30.pc_transcripts.fa.fai added
145b44b88c6a_gencode.vM31.pc_transcripts.fa added
145b300aa665_gencode.vM31.pc_transcripts.fa.fai added
145bb324987_GRCh38.primary_assembly.genome.fa.1.ht2 added
145b127943cf_GRCh38.primary_assembly.genome.fa.2.ht2 added
145b5752d482_GRCh38.primary_assembly.genome.fa.3.ht2 added
145b7efdcf97_GRCh38.primary_assembly.genome.fa.4.ht2 added
145b494803a3_GRCh38.primary_assembly.genome.fa.5.ht2 added
145b16e6e7eb_GRCh38.primary_assembly.genome.fa.6.ht2 added
145b1184010c_GRCh38.primary_assembly.genome.fa.7.ht2 added
145b7160c3cf_GRCh38.primary_assembly.genome.fa.8.ht2 added
145b7d78530_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
145b56691655_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
145bd3952c5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
145b2e690a4b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
145b7222d9ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
145b4e047ce0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
145b8a27e24_GRCh38_full_analysis_set_plus_decoy_hla.fa added
145b640771e9_GRCh38.primary_assembly.genome.fa.fai added
145b24c7ab4d_GRCh38.primary_assembly.genome.fa.amb added
145b30bf5f18_GRCh38.primary_assembly.genome.fa.ann added
145b63fc39a8_GRCh38.primary_assembly.genome.fa.bwt added
145b442d77e0_GRCh38.primary_assembly.genome.fa.pac added
145b5193618_GRCh38.primary_assembly.genome.fa.sa added
145b3a2e6445_GRCh38.primary_assembly.genome.fa added
145b3bb90bda_hs37d5.fa.fai added
145b71b933d7_hs37d5.fa.amb added
145b35faa295_hs37d5.fa.ann added
145b59c7ffe2_hs37d5.fa.bwt added
145b59707c7a_hs37d5.fa.pac added
145b67fc5b75_hs37d5.fa.sa added
145b68d893a8_hs37d5.fa added
145b62c6305e_complete_ref_lens.bin added
145b41919dfb_ctable.bin added
145b3f1aeb5e_ctg_offsets.bin added
145b5288b0_duplicate_clusters.tsv added
145b2a8bdafa_info.json added
145b43d568e8_mphf.bin added
145b6fda7a22_pos.bin added
145b7088878c_pre_indexing.log added
145b137b320c_rank.bin added
145b7d12bbd1_ref_indexing.log added
145b58e8d67d_refAccumLengths.bin added
145b1e59d625_reflengths.bin added
145b1bfa26b4_refseq.bin added
145b440301c5_seq.bin added
145b21694f65_versionInfo.json added
145b8db8106_salmon_index added
145b2f3b575_chrLength.txt added
145b4e0e15d6_chrName.txt added
145b7ebbbca2_chrNameLength.txt added
145b575d70ae_chrStart.txt added
145b3790dc51_exonGeTrInfo.tab added
145b7706657_exonInfo.tab added
145b644edd91_geneInfo.tab added
145b75b48e09_Genome added
145b20d92d3e_genomeParameters.txt added
145b1229524b_Log.out added
145b56d9c33d_SA added
145b72a10656_SAindex added
145b29a732e5_sjdbInfo.txt added
145b1ffe6dc0_sjdbList.fromGTF.out.tab added
145b78d768a8_sjdbList.out.tab added
145b6182b93_transcriptInfo.tab added
145b1cd4c305_GRCh38.GENCODE.v42_100 added
145b544f8c0c_knownGene_hg38.sql added
145b32739312_knownGene_hg38.txt added
145b41bc9c9e_refGene_hg38.sql added
145b45ce6ac9_refGene_hg38.txt added
145b72c4d5ec_knownGene_mm39.sql added
145b58b8b3d1_knownGene_mm39.txt added
145b46258bd8_refGene_mm39.sql added
145b4b0035e2_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/RtmpjZdSiA/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
25.024 3.161 29.575
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.940 | 0.941 | 9.029 | |
| dataSearch | 1.430 | 0.061 | 1.508 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.950 | 0.155 | 4.069 | |
| getData | 0.001 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.152 | 0.013 | 0.167 | |
| recipeLoad | 1.618 | 0.107 | 1.746 | |
| recipeMake | 0.000 | 0.002 | 0.002 | |
| recipeSearch | 0.731 | 0.048 | 0.789 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |