Qian Liu
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: d45ef48 |
| git_last_commit_date: 2023-11-22 22:25:57 -0400 (Wed, 22 Nov 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:58 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1723/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.3.2 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | 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: 1.3.2 |
| 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_1.3.2.tar.gz |
| StartedAt: 2024-03-28 01:59:43 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 02:02:37 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 173.3 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘1.3.2’
* 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 6.09 0.376 6.468
* 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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...
23c62a52236266_GRCh38.primary_assembly.genome.fa.1.bt2 added
23c62a6cbb7801_GRCh38.primary_assembly.genome.fa.2.bt2 added
23c62a15f60b08_GRCh38.primary_assembly.genome.fa.3.bt2 added
23c62a7010492f_GRCh38.primary_assembly.genome.fa.4.bt2 added
23c62a12f67cf3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
23c62a68cde6c1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
23c62a52b333fa_outfile.txt added
23c62a9e9e014_GRCh37_to_GRCh38.chain added
23c62aac7a4f0_GRCh37_to_NCBI34.chain added
23c62a62b7bb02_GRCh37_to_NCBI35.chain added
23c62a2cd09b99_GRCh37_to_NCBI36.chain added
23c62a2e64387e_GRCh38_to_GRCh37.chain added
23c62a5820c82d_GRCh38_to_NCBI34.chain added
23c62a614c0c49_GRCh38_to_NCBI35.chain added
23c62a70efa677_GRCh38_to_NCBI36.chain added
23c62a746d6b17_NCBI34_to_GRCh37.chain added
23c62a1871f222_NCBI34_to_GRCh38.chain added
23c62a5be4cd3d_NCBI35_to_GRCh37.chain added
23c62a395d9f99_NCBI35_to_GRCh38.chain added
23c62a5e14f631_NCBI36_to_GRCh37.chain added
23c62a131e5807_NCBI36_to_GRCh38.chain added
23c62a799ad4e5_GRCm38_to_NCBIM36.chain added
23c62a2fd3a64d_GRCm38_to_NCBIM37.chain added
23c62a785c9618_NCBIM36_to_GRCm38.chain added
23c62a5aee7360_NCBIM37_to_GRCm38.chain added
23c62a3617af05_1000G_omni2.5.b37.vcf.gz added
23c62a5a4d5c55_1000G_omni2.5.b37.vcf.gz.tbi added
23c62a7ab0ab9f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
23c62a6a5acdbd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
23c62a58354eb3_1000G_omni2.5.hg38.vcf.gz added
23c62a650d3f26_1000G_omni2.5.hg38.vcf.gz.tbi added
23c62a3c7e3023_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
23c62a44f0c6b5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
23c62a7b034a2e_af-only-gnomad.raw.sites.vcf added
23c62a2c8e7952_af-only-gnomad.raw.sites.vcf.idx added
23c62a57e743a8_Mutect2-exome-panel.vcf.idx added
23c62a63d130f0_Mutect2-WGS-panel-b37.vcf added
23c62a7f41ad4d_Mutect2-WGS-panel-b37.vcf.idx added
23c62a61d123bc_small_exac_common_3.vcf added
23c62a6e98d5e0_small_exac_common_3.vcf.idx added
23c62a61f9684f_1000g_pon.hg38.vcf.gz added
23c62aea1bf55_1000g_pon.hg38.vcf.gz.tbi added
23c62a1cfd0e5e_af-only-gnomad.hg38.vcf.gz added
23c62a3a1a307c_af-only-gnomad.hg38.vcf.gz.tbi added
23c62a6fedcb9f_small_exac_common_3.hg38.vcf.gz added
23c62adecb4d5_small_exac_common_3.hg38.vcf.gz.tbi added
23c62a2e879b93_gencode.v41.annotation.gtf added
23c62a85fbdc1_gencode.v42.annotation.gtf added
23c62a69d18213_gencode.vM30.annotation.gtf added
23c62a67e53b2c_gencode.vM31.annotation.gtf added
23c62a6674b3f2_gencode.v41.transcripts.fa added
23c62a7cefda1a_gencode.v41.transcripts.fa.fai added
23c62a61801011_gencode.v42.transcripts.fa added
23c62a16485a3f_gencode.v42.transcripts.fa.fai added
23c62a754c7033_gencode.vM30.pc_transcripts.fa added
23c62a3c6e8371_gencode.vM30.pc_transcripts.fa.fai added
23c62a4c600945_gencode.vM31.pc_transcripts.fa added
23c62a4f99cc88_gencode.vM31.pc_transcripts.fa.fai added
23c62a371f2f11_GRCh38.primary_assembly.genome.fa.1.ht2 added
23c62a36bad702_GRCh38.primary_assembly.genome.fa.2.ht2 added
23c62a27cf1b3c_GRCh38.primary_assembly.genome.fa.3.ht2 added
23c62a1c2c6e37_GRCh38.primary_assembly.genome.fa.4.ht2 added
23c62a73390725_GRCh38.primary_assembly.genome.fa.5.ht2 added
23c62a6cbfe1f1_GRCh38.primary_assembly.genome.fa.6.ht2 added
23c62a172fb866_GRCh38.primary_assembly.genome.fa.7.ht2 added
23c62a1fc78078_GRCh38.primary_assembly.genome.fa.8.ht2 added
23c62a44a72599_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
23c62a7b00e956_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
23c62a1f092dc5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
23c62a26784955_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
23c62a6999bf36_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
23c62a1029614_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
23c62a351a08ab_GRCh38_full_analysis_set_plus_decoy_hla.fa added
23c62a696cd94_GRCh38.primary_assembly.genome.fa.fai added
23c62a3b1cc690_GRCh38.primary_assembly.genome.fa.amb added
23c62a2507d44a_GRCh38.primary_assembly.genome.fa.ann added
23c62a14838269_GRCh38.primary_assembly.genome.fa.bwt added
23c62a69a46223_GRCh38.primary_assembly.genome.fa.pac added
23c62a2d67920b_GRCh38.primary_assembly.genome.fa.sa added
23c62a7e55047c_GRCh38.primary_assembly.genome.fa added
23c62a51899d4f_hs37d5.fa.fai added
23c62a13dc45fd_hs37d5.fa.amb added
23c62a7b44de97_hs37d5.fa.ann added
23c62a3309ad61_hs37d5.fa.bwt added
23c62a2a24a03d_hs37d5.fa.pac added
23c62a70914eca_hs37d5.fa.sa added
23c62a6f7830d2_hs37d5.fa added
23c62a7684a982_complete_ref_lens.bin added
23c62a402b1b52_ctable.bin added
23c62a26975fe3_ctg_offsets.bin added
23c62a2d3f8084_duplicate_clusters.tsv added
23c62a67fa368e_info.json added
23c62a42c3ce1b_mphf.bin added
23c62a207887a9_pos.bin added
23c62a54ba187f_pre_indexing.log added
23c62a59f38681_rank.bin added
23c62a40400821_ref_indexing.log added
23c62a19613e18_refAccumLengths.bin added
23c62a54f46fd7_reflengths.bin added
23c62a5f4935e6_refseq.bin added
23c62a3fd9876e_seq.bin added
23c62a3e8e2f0d_versionInfo.json added
23c62a604bcbfa_salmon_index added
23c62a74f39019_chrLength.txt added
23c62a4524fca1_chrName.txt added
23c62a1b68928a_chrNameLength.txt added
23c62a19fb6463_chrStart.txt added
23c62a59a87f0a_exonGeTrInfo.tab added
23c62a50cf4ad_exonInfo.tab added
23c62a4762f66e_geneInfo.tab added
23c62a57fd8387_Genome added
23c62a569691fd_genomeParameters.txt added
23c62a5b3f3c6b_Log.out added
23c62a5342621e_SA added
23c62a9a03f5e_SAindex added
23c62a563dca8_sjdbInfo.txt added
23c62a43d3b0e8_sjdbList.fromGTF.out.tab added
23c62a79187030_sjdbList.out.tab added
23c62a7be8862a_transcriptInfo.tab added
23c62a3fecc3a_GRCh38.GENCODE.v42_100 added
23c62a1fafd014_knownGene_hg38.sql added
23c62a292806ae_knownGene_hg38.txt added
23c62a6bf902c9_refGene_hg38.sql added
23c62a62739e2f_refGene_hg38.txt added
23c62a49a08e58_knownGene_mm39.sql added
23c62a40b31b48_knownGene_mm39.txt added
23c62a3c6724b0_refGene_mm39.sql added
23c62a9e09679_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/RtmpWzzUzP/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
19.926 1.751 21.992
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.090 | 0.376 | 6.468 | |
| dataSearch | 1.114 | 0.051 | 1.166 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.673 | 0.072 | 3.225 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.137 | 0.000 | 0.138 | |
| recipeLoad | 1.302 | 0.024 | 1.327 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.586 | 0.012 | 0.599 | |
| recipeUpdate | 0 | 0 | 0 | |