Qian Liu
| Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 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 2024-07-24 09:03 -0400 (Wed, 24 Jul 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" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz |
| StartedAt: 2024-07-22 04:12:03 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 04:14:54 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 171.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 6.297 0.397 6.695
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-pc-linux-gnu
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...
3a55497fe0a14b_GRCh38.primary_assembly.genome.fa.1.bt2 added
3a5549334f35df_GRCh38.primary_assembly.genome.fa.2.bt2 added
3a554926ba2495_GRCh38.primary_assembly.genome.fa.3.bt2 added
3a5549736e356_GRCh38.primary_assembly.genome.fa.4.bt2 added
3a554954b311a5_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3a55493eab7c78_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3a5549471a9a8_outfile.txt added
3a55494480e594_GRCh37_to_GRCh38.chain added
3a554935960cd1_GRCh37_to_NCBI34.chain added
3a5549a4d9959_GRCh37_to_NCBI35.chain added
3a5549674b3aef_GRCh37_to_NCBI36.chain added
3a55497ff1f177_GRCh38_to_GRCh37.chain added
3a55491a355f7a_GRCh38_to_NCBI34.chain added
3a5549400aa4d0_GRCh38_to_NCBI35.chain added
3a55494783b6ee_GRCh38_to_NCBI36.chain added
3a5549520a770c_NCBI34_to_GRCh37.chain added
3a55492f26c88b_NCBI34_to_GRCh38.chain added
3a5549585eeb56_NCBI35_to_GRCh37.chain added
3a554973263194_NCBI35_to_GRCh38.chain added
3a55497bbd0b75_NCBI36_to_GRCh37.chain added
3a554956d6ddcf_NCBI36_to_GRCh38.chain added
3a55497c887bb0_GRCm38_to_NCBIM36.chain added
3a55494b6df571_GRCm38_to_NCBIM37.chain added
3a55493539f60f_NCBIM36_to_GRCm38.chain added
3a55493a65e79_NCBIM37_to_GRCm38.chain added
3a5549795de976_1000G_omni2.5.b37.vcf.gz added
3a5549405c776b_1000G_omni2.5.b37.vcf.gz.tbi added
3a5549a5d6753_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3a55494e53d655_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3a55496bb655e0_1000G_omni2.5.hg38.vcf.gz added
3a55493da23e3f_1000G_omni2.5.hg38.vcf.gz.tbi added
3a55494e3477a0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3a55491f058bc0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3a5549645c62d4_af-only-gnomad.raw.sites.vcf added
3a5549556b5af7_af-only-gnomad.raw.sites.vcf.idx added
3a554973b89d65_Mutect2-exome-panel.vcf.idx added
3a55492307df4c_Mutect2-WGS-panel-b37.vcf added
3a554959dd049f_Mutect2-WGS-panel-b37.vcf.idx added
3a5549383982fa_small_exac_common_3.vcf added
3a5549589dec1d_small_exac_common_3.vcf.idx added
3a5549642a9df9_1000g_pon.hg38.vcf.gz added
3a55491f84bde9_1000g_pon.hg38.vcf.gz.tbi added
3a5549588fdd94_af-only-gnomad.hg38.vcf.gz added
3a55497e5ffd73_af-only-gnomad.hg38.vcf.gz.tbi added
3a55495f8f62ba_small_exac_common_3.hg38.vcf.gz added
3a554920139483_small_exac_common_3.hg38.vcf.gz.tbi added
3a5549506a747f_gencode.v41.annotation.gtf added
3a5549eb62b45_gencode.v42.annotation.gtf added
3a554978727fd9_gencode.vM30.annotation.gtf added
3a55494390a613_gencode.vM31.annotation.gtf added
3a5549a7336bb_gencode.v41.transcripts.fa added
3a55494f495da8_gencode.v41.transcripts.fa.fai added
3a5549401921c3_gencode.v42.transcripts.fa added
3a554955e12c2c_gencode.v42.transcripts.fa.fai added
3a554948353b8_gencode.vM30.pc_transcripts.fa added
3a554943bf803d_gencode.vM30.pc_transcripts.fa.fai added
3a55494f3f15a2_gencode.vM31.pc_transcripts.fa added
3a554944dfcb23_gencode.vM31.pc_transcripts.fa.fai added
3a55494e1ce790_GRCh38.primary_assembly.genome.fa.1.ht2 added
3a55491d92ebf8_GRCh38.primary_assembly.genome.fa.2.ht2 added
3a554930962103_GRCh38.primary_assembly.genome.fa.3.ht2 added
3a5549bbf25cf_GRCh38.primary_assembly.genome.fa.4.ht2 added
3a55496bc76398_GRCh38.primary_assembly.genome.fa.5.ht2 added
3a55494f9bacc3_GRCh38.primary_assembly.genome.fa.6.ht2 added
3a5549701b88a3_GRCh38.primary_assembly.genome.fa.7.ht2 added
3a55494132be8f_GRCh38.primary_assembly.genome.fa.8.ht2 added
3a554943544a29_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3a5549132367ef_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3a55491b0fc32f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3a55497b8dcd23_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3a55496bc1540c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3a55497f3a6128_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3a55491b128b0c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3a5549445131a1_GRCh38.primary_assembly.genome.fa.fai added
3a55497d9a5e9b_GRCh38.primary_assembly.genome.fa.amb added
3a55497aa1edc6_GRCh38.primary_assembly.genome.fa.ann added
3a55496464c624_GRCh38.primary_assembly.genome.fa.bwt added
3a55494e04d31a_GRCh38.primary_assembly.genome.fa.pac added
3a5549958190c_GRCh38.primary_assembly.genome.fa.sa added
3a55495cd745fd_GRCh38.primary_assembly.genome.fa added
3a55491195792e_hs37d5.fa.fai added
3a554913cb4fc7_hs37d5.fa.amb added
3a55492c20a3a5_hs37d5.fa.ann added
3a554951ae9af1_hs37d5.fa.bwt added
3a554969ac7bf3_hs37d5.fa.pac added
3a554930a3f75d_hs37d5.fa.sa added
3a5549156e1b2e_hs37d5.fa added
3a554938eb9196_complete_ref_lens.bin added
3a55497583c280_ctable.bin added
3a5549638b02bf_ctg_offsets.bin added
3a5549567e7d8e_duplicate_clusters.tsv added
3a55492619e384_info.json added
3a55496f4a288e_mphf.bin added
3a55494245e126_pos.bin added
3a554975b59047_pre_indexing.log added
3a55495f65b132_rank.bin added
3a55493789fb6_ref_indexing.log added
3a55493909da70_refAccumLengths.bin added
3a554972891921_reflengths.bin added
3a55491e8862e5_refseq.bin added
3a55493497a793_seq.bin added
3a55495e4a6d2e_versionInfo.json added
3a55491dc2c40d_salmon_index added
3a55494faa32a0_chrLength.txt added
3a5549229b9ecf_chrName.txt added
3a55491b5d22a8_chrNameLength.txt added
3a55494a4c2066_chrStart.txt added
3a554970064f3_exonGeTrInfo.tab added
3a55496961f5c2_exonInfo.tab added
3a554953a43972_geneInfo.tab added
3a554963d7aaf0_Genome added
3a55497af76ef0_genomeParameters.txt added
3a5549676f8939_Log.out added
3a5549ff84e95_SA added
3a55494ca609e2_SAindex added
3a5549511c052d_sjdbInfo.txt added
3a5549409c45f3_sjdbList.fromGTF.out.tab added
3a554962142510_sjdbList.out.tab added
3a5549a0796c3_transcriptInfo.tab added
3a554936200873_GRCh38.GENCODE.v42_100 added
3a5549459f27cf_knownGene_hg38.sql added
3a554960861451_knownGene_hg38.txt added
3a55495c39ebf7_refGene_hg38.sql added
3a554934e9505e_refGene_hg38.txt added
3a554922cbf577_knownGene_mm39.sql added
3a554951ef7c3f_knownGene_mm39.txt added
3a5549144f0190_refGene_mm39.sql added
3a55492644952d_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/Rtmp9wJwg5/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
19.222 1.418 21.076
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.297 | 0.397 | 6.695 | |
| dataSearch | 1.147 | 0.068 | 1.214 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.739 | 0.116 | 3.613 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.118 | 0.012 | 0.130 | |
| recipeLoad | 1.265 | 0.092 | 1.359 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.527 | 0.024 | 0.552 | |
| recipeUpdate | 0 | 0 | 0 | |