Qian Liu
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_20 |
| git_last_commit: 5d8c0ee |
| git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 1727/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.6.0 (landing page) Qian Liu
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2024-11-20 01:48:19 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 01:54:08 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 348.7 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_1.6.0.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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 6.605 0.849 7.617
* 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...
15f4452b2d8ba_GRCh38.primary_assembly.genome.fa.1.bt2 added
15f445bb2c5c0_GRCh38.primary_assembly.genome.fa.2.bt2 added
15f4435d4ef48_GRCh38.primary_assembly.genome.fa.3.bt2 added
15f442ea97b94_GRCh38.primary_assembly.genome.fa.4.bt2 added
15f4478f0497a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
15f446768269d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
15f4466bf4274_outfile.txt added
15f4416a4025f_GRCh37_to_GRCh38.chain added
15f446997b695_GRCh37_to_NCBI34.chain added
15f446754265b_GRCh37_to_NCBI35.chain added
15f4445a2555c_GRCh37_to_NCBI36.chain added
15f4424922ebb_GRCh38_to_GRCh37.chain added
15f44793a09be_GRCh38_to_NCBI34.chain added
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15f445a9e5df0_GRCh38_to_NCBI36.chain added
15f445329660a_NCBI34_to_GRCh37.chain added
15f4442ea452d_NCBI34_to_GRCh38.chain added
15f442263afad_NCBI35_to_GRCh37.chain added
15f443ea2987e_NCBI35_to_GRCh38.chain added
15f4424c99852_NCBI36_to_GRCh37.chain added
15f442f2f425c_NCBI36_to_GRCh38.chain added
15f4447adbe37_GRCm38_to_NCBIM36.chain added
15f445fa331a4_GRCm38_to_NCBIM37.chain added
15f4453103709_NCBIM36_to_GRCm38.chain added
15f444d8d5a79_NCBIM37_to_GRCm38.chain added
15f447b2ee5b5_1000G_omni2.5.b37.vcf.gz added
15f4443eb0d41_1000G_omni2.5.b37.vcf.gz.tbi added
15f447cb3493c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
15f445e8d4219_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
15f44beea7ce_1000G_omni2.5.hg38.vcf.gz added
15f44614acb80_1000G_omni2.5.hg38.vcf.gz.tbi added
15f4475767266_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
15f443350c2c9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
15f447b243470_af-only-gnomad.raw.sites.vcf added
15f445eee439_af-only-gnomad.raw.sites.vcf.idx added
15f446c95d3a_Mutect2-exome-panel.vcf.idx added
15f44e078e51_Mutect2-WGS-panel-b37.vcf added
15f4412106f09_Mutect2-WGS-panel-b37.vcf.idx added
15f4474e9c122_small_exac_common_3.vcf added
15f441e86db25_small_exac_common_3.vcf.idx added
15f44279d69cb_1000g_pon.hg38.vcf.gz added
15f444f8ca2be_1000g_pon.hg38.vcf.gz.tbi added
15f441a1090bf_af-only-gnomad.hg38.vcf.gz added
15f44358ef8f7_af-only-gnomad.hg38.vcf.gz.tbi added
15f443d7b3b99_small_exac_common_3.hg38.vcf.gz added
15f446585d957_small_exac_common_3.hg38.vcf.gz.tbi added
15f44368012d3_gencode.v41.annotation.gtf added
15f441253f699_gencode.v42.annotation.gtf added
15f444662c035_gencode.vM30.annotation.gtf added
15f447d38fbac_gencode.vM31.annotation.gtf added
15f442813196e_gencode.v41.transcripts.fa added
15f447dea994f_gencode.v41.transcripts.fa.fai added
15f4434f7521e_gencode.v42.transcripts.fa added
15f4459304abc_gencode.v42.transcripts.fa.fai added
15f44717aaa62_gencode.vM30.pc_transcripts.fa added
15f442c484222_gencode.vM30.pc_transcripts.fa.fai added
15f443beddce4_gencode.vM31.pc_transcripts.fa added
15f447d411b78_gencode.vM31.pc_transcripts.fa.fai added
15f443d72a386_GRCh38.primary_assembly.genome.fa.1.ht2 added
15f44314dd1ee_GRCh38.primary_assembly.genome.fa.2.ht2 added
15f446c11798b_GRCh38.primary_assembly.genome.fa.3.ht2 added
15f446f42cc1a_GRCh38.primary_assembly.genome.fa.4.ht2 added
15f44a65f807_GRCh38.primary_assembly.genome.fa.5.ht2 added
15f442c7e98e6_GRCh38.primary_assembly.genome.fa.6.ht2 added
15f442b683adc_GRCh38.primary_assembly.genome.fa.7.ht2 added
15f4447f057c7_GRCh38.primary_assembly.genome.fa.8.ht2 added
15f447412eeb6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
15f446f62a43_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
15f44b509847_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
15f44583d631e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
15f44263673d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
15f4440ee76e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
15f4467bfd5b0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
15f4463664b06_GRCh38.primary_assembly.genome.fa.fai added
15f4450c7a9e5_GRCh38.primary_assembly.genome.fa.amb added
15f44646322d1_GRCh38.primary_assembly.genome.fa.ann added
15f442882fad4_GRCh38.primary_assembly.genome.fa.bwt added
15f442f218913_GRCh38.primary_assembly.genome.fa.pac added
15f4442ae5691_GRCh38.primary_assembly.genome.fa.sa added
15f4443b56bca_GRCh38.primary_assembly.genome.fa added
15f443bb7bd80_hs37d5.fa.fai added
15f441bfa3d21_hs37d5.fa.amb added
15f4449c34fe0_hs37d5.fa.ann added
15f4435b120f5_hs37d5.fa.bwt added
15f447fead05c_hs37d5.fa.pac added
15f44111589a0_hs37d5.fa.sa added
15f441cfe7023_hs37d5.fa added
15f4447418b4_complete_ref_lens.bin added
15f446201d3b4_ctable.bin added
15f4465f200b0_ctg_offsets.bin added
15f44730b5719_duplicate_clusters.tsv added
15f446d836550_info.json added
15f444d709f5b_mphf.bin added
15f441cee3715_pos.bin added
15f445b625289_pre_indexing.log added
15f441418cf3e_rank.bin added
15f4468cdf9c0_ref_indexing.log added
15f442ac7e201_refAccumLengths.bin added
15f4428c6c598_reflengths.bin added
15f4411d69312_refseq.bin added
15f441e518be4_seq.bin added
15f447bb73548_versionInfo.json added
15f44390b496c_salmon_index added
15f4414016eb6_chrLength.txt added
15f446a0b78fc_chrName.txt added
15f4417341ec8_chrNameLength.txt added
15f445ed0e85e_chrStart.txt added
15f446547a3f3_exonGeTrInfo.tab added
15f44425cda77_exonInfo.tab added
15f445e0adcaa_geneInfo.tab added
15f441b1d4d22_Genome added
15f4420b30116_genomeParameters.txt added
15f44480c5c1f_Log.out added
15f4423741c2d_SA added
15f441be5e08a_SAindex added
15f4410f89255_sjdbInfo.txt added
15f442f4f1327_sjdbList.fromGTF.out.tab added
15f4470727db4_sjdbList.out.tab added
15f446c9aee18_transcriptInfo.tab added
15f442f85a15c_GRCh38.GENCODE.v42_100 added
15f446e24b763_knownGene_hg38.sql added
15f442c83fd13_knownGene_hg38.txt added
15f44d5c013a_refGene_hg38.sql added
15f4413548db0_refGene_hg38.txt added
15f44142227ba_knownGene_mm39.sql added
15f444e5e2ea9_knownGene_mm39.txt added
15f449498171_refGene_mm39.sql added
15f4438d1267a_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/RtmpAMSxpV/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
18.612 2.653 22.529
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.605 | 0.849 | 7.617 | |
| dataSearch | 1.286 | 0.060 | 1.363 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.307 | 0.130 | 3.235 | |
| getData | 0.001 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.126 | 0.010 | 0.138 | |
| recipeLoad | 1.232 | 0.085 | 1.331 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.556 | 0.039 | 0.603 | |
| recipeUpdate | 0 | 0 | 0 | |