Qian Liu
| Snapshot Date: 2024-06-30 14:00 -0400 (Sun, 30 Jun 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 2024-07-03 10:23 -0400 (Wed, 03 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
| 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 12.7.4 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: /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_1.4.0.tar.gz |
| StartedAt: 2024-07-02 07:04:38 -0400 (Tue, 02 Jul 2024) |
| EndedAt: 2024-07-02 07:07:04 -0400 (Tue, 02 Jul 2024) |
| EllapsedTime: 145.9 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 6.583 0.744 7.379
* 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-3.19-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-arm64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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...
107087062dd6f_GRCh38.primary_assembly.genome.fa.1.bt2 added
107086ab7dc0d_GRCh38.primary_assembly.genome.fa.2.bt2 added
107084cd01037_GRCh38.primary_assembly.genome.fa.3.bt2 added
107086fd8b246_GRCh38.primary_assembly.genome.fa.4.bt2 added
107087ba04b07_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
10708589df7f9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
107086b0329e2_outfile.txt added
107081cb2eb51_GRCh37_to_GRCh38.chain added
107082677218f_GRCh37_to_NCBI34.chain added
10708573c4703_GRCh37_to_NCBI35.chain added
10708365a42b3_GRCh37_to_NCBI36.chain added
107085fd111a5_GRCh38_to_GRCh37.chain added
1070816dd98c8_GRCh38_to_NCBI34.chain added
107082e597e32_GRCh38_to_NCBI35.chain added
10708756c1c63_GRCh38_to_NCBI36.chain added
10708cbbe3cf_NCBI34_to_GRCh37.chain added
107083693191_NCBI34_to_GRCh38.chain added
107086f352856_NCBI35_to_GRCh37.chain added
10708aeb5f24_NCBI35_to_GRCh38.chain added
1070862b33a15_NCBI36_to_GRCh37.chain added
1070864aa6b52_NCBI36_to_GRCh38.chain added
10708706c081f_GRCm38_to_NCBIM36.chain added
10708448964e2_GRCm38_to_NCBIM37.chain added
10708183e5495_NCBIM36_to_GRCm38.chain added
1070824230ea2_NCBIM37_to_GRCm38.chain added
107087995c036_1000G_omni2.5.b37.vcf.gz added
10708567e5796_1000G_omni2.5.b37.vcf.gz.tbi added
10708a86537_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
107082f8cfe37_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
107085185e544_1000G_omni2.5.hg38.vcf.gz added
107082d8efd2c_1000G_omni2.5.hg38.vcf.gz.tbi added
1070868f6b12_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1070831be6e1b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
107084d2ec820_af-only-gnomad.raw.sites.vcf added
107083a54d476_af-only-gnomad.raw.sites.vcf.idx added
107081748ace5_Mutect2-exome-panel.vcf.idx added
10708244efa54_Mutect2-WGS-panel-b37.vcf added
107083d14b36b_Mutect2-WGS-panel-b37.vcf.idx added
107081a0f5521_small_exac_common_3.vcf added
10708649df6e4_small_exac_common_3.vcf.idx added
107083ebc2657_1000g_pon.hg38.vcf.gz added
10708327939ee_1000g_pon.hg38.vcf.gz.tbi added
1070834ca5225_af-only-gnomad.hg38.vcf.gz added
107084ed71636_af-only-gnomad.hg38.vcf.gz.tbi added
10708af35baa_small_exac_common_3.hg38.vcf.gz added
107086f06fb83_small_exac_common_3.hg38.vcf.gz.tbi added
10708336a8e67_gencode.v41.annotation.gtf added
1070818ab2690_gencode.v42.annotation.gtf added
10708c70c497_gencode.vM30.annotation.gtf added
107083f7a9be2_gencode.vM31.annotation.gtf added
10708a9032fd_gencode.v41.transcripts.fa added
107081038576_gencode.v41.transcripts.fa.fai added
10708e2f067f_gencode.v42.transcripts.fa added
107083153831f_gencode.v42.transcripts.fa.fai added
1070861c58185_gencode.vM30.pc_transcripts.fa added
107086dba74e8_gencode.vM30.pc_transcripts.fa.fai added
107086c51639f_gencode.vM31.pc_transcripts.fa added
1070853639347_gencode.vM31.pc_transcripts.fa.fai added
107082e5a4516_GRCh38.primary_assembly.genome.fa.1.ht2 added
10708286dbf20_GRCh38.primary_assembly.genome.fa.2.ht2 added
107083d1ee29c_GRCh38.primary_assembly.genome.fa.3.ht2 added
1070836af8f1d_GRCh38.primary_assembly.genome.fa.4.ht2 added
107083fdcd4f7_GRCh38.primary_assembly.genome.fa.5.ht2 added
107083b21c4e2_GRCh38.primary_assembly.genome.fa.6.ht2 added
107082604efc2_GRCh38.primary_assembly.genome.fa.7.ht2 added
10708e18bd0e_GRCh38.primary_assembly.genome.fa.8.ht2 added
107087a23e95c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
107084badd5a9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
107081a67110_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
107085648d248_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1070846e5a139_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
10708dbbc98c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1070823ad0d5f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
107083648ea45_GRCh38.primary_assembly.genome.fa.fai added
107086d0c73da_GRCh38.primary_assembly.genome.fa.amb added
107084c8a2524_GRCh38.primary_assembly.genome.fa.ann added
1070818c85be_GRCh38.primary_assembly.genome.fa.bwt added
1070830a07dbd_GRCh38.primary_assembly.genome.fa.pac added
10708789f1c3b_GRCh38.primary_assembly.genome.fa.sa added
1070815f6a35b_GRCh38.primary_assembly.genome.fa added
10708735eb6a0_hs37d5.fa.fai added
107084f27fd8c_hs37d5.fa.amb added
107084a771aed_hs37d5.fa.ann added
107085188e3cc_hs37d5.fa.bwt added
1070872238fe5_hs37d5.fa.pac added
107087cbc3ded_hs37d5.fa.sa added
107082a85d295_hs37d5.fa added
1070837c44a02_complete_ref_lens.bin added
1070837d6e5e8_ctable.bin added
107087d8ffefb_ctg_offsets.bin added
1070878ad5123_duplicate_clusters.tsv added
107083aaa0eba_info.json added
1070872acf36c_mphf.bin added
1070838a17245_pos.bin added
107086f552d0e_pre_indexing.log added
1070841012b3c_rank.bin added
1070833bd917b_ref_indexing.log added
10708629a3cc6_refAccumLengths.bin added
107087c0c1dbc_reflengths.bin added
107087f746143_refseq.bin added
10708319db714_seq.bin added
10708695e9b7e_versionInfo.json added
107084232a33d_salmon_index added
10708a7b1bbf_chrLength.txt added
10708185a9df9_chrName.txt added
10708653952ec_chrNameLength.txt added
10708167337df_chrStart.txt added
1070866591cfc_exonGeTrInfo.tab added
10708647e18e2_exonInfo.tab added
107081293d0f9_geneInfo.tab added
10708267c94f6_Genome added
107083d17b637_genomeParameters.txt added
107085fbbf436_Log.out added
107082c9e3654_SA added
107084700dbae_SAindex added
10708956a0ed_sjdbInfo.txt added
10708165f2c65_sjdbList.fromGTF.out.tab added
10708425ba65c_sjdbList.out.tab added
10708f07040d_transcriptInfo.tab added
10708159af930_GRCh38.GENCODE.v42_100 added
10708715dc964_knownGene_hg38.sql added
107084450fe61_knownGene_hg38.txt added
10708216cb551_refGene_hg38.sql added
1070867f3e9fb_refGene_hg38.txt added
107083e86930e_knownGene_mm39.sql added
1070875209c33_knownGene_mm39.txt added
107082fef1458_refGene_mm39.sql added
107087920b5fd_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/RtmpL3kt2i/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
24.204 2.931 28.638
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.583 | 0.744 | 7.379 | |
| dataSearch | 1.166 | 0.055 | 1.226 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.831 | 0.144 | 4.838 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.146 | 0.013 | 0.160 | |
| recipeLoad | 1.446 | 0.107 | 1.559 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.683 | 0.039 | 0.726 | |
| recipeUpdate | 0 | 0 | 0 | |