Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:17 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the RNASeqR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNASeqR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1709/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Kuan-Hao Chao
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: RNASeqR |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RNASeqR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings RNASeqR_1.16.0.tar.gz |
StartedAt: 2023-04-10 23:31:48 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 23:37:56 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 368.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: RNASeqR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RNASeqR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings RNASeqR_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/RNASeqR.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘RNASeqR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RNASeqR’ version ‘1.16.0’ * 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 ‘RNASeqR’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'RNASeqR' is deprecated and will be removed from Bioconductor See ‘/home/biocbuild/bbs-3.16-bioc/meat/RNASeqR.Rcheck/00install.out’ for details. * 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 R 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 ... NOTE AlignmentPlot: no visible binding for global variable ‘value’ Update_Fastq_gz: no visible binding for global variable ‘sample.pattern’ Undefined global functions or variables: sample.pattern value * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... ERROR Running examples in ‘RNASeqR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: RNASeqRParam-constructor > ### Title: RNASeqRParam > ### Aliases: RNASeqRParam-constructor RNASeqRParam > > ### ** Examples > > input_files.path <- system.file("extdata/", package = "RNASeqRData") > rnaseq_result.path <- tempdir(check = TRUE) > exp <- RNASeqRParam(path.prefix = rnaseq_result.path, + input.path.prefix = input_files.path, + genome.name = "Saccharomyces_cerevisiae_XV_Ensembl", + sample.pattern = "SRR[0-9]*_XV", + independent.variable = "state", + case.group = "60mins_ID20_amphotericin_B", + control.group = "60mins_ID20_control", + fastq.gz.type = "PE") ************** Checking input parameters ************ (✔) : Input parameters are all not NA !! ************** Checking operating system type ************ (✔) : Your system operating system is 'linux' ************** Checking python version ************ (✔) : Python is available on your device! ● Python version : 3.8 ************** Checking 2to3 command ************ sh: 1: 2to3: not found Warning in system2("2to3", "--help", stdout = FALSE) : error in running command (✘) : 2to3 command is not available on your device! ************** Setting prefix path ************ (✎) : The following files will be installed under '/tmp/RtmpbweMZH/' ************** Setting input prefix path ************ (✎) : 'input_files' is found under '/home/biocbuild/bbs-3.16-bioc/R/site-library/RNASeqRData/extdata/' directory. ● Validity of 'input_files/' will be checked. ************** Checking phenodata ************ ▶ Checking whether "raw_fastq.gz files" matches "'ids' of phenodata.csv" (✔) : Column 'ids' of phenodata.csv is valid. ● sample ids are : "SRR3396381_XV, SRR3396382_XV, SRR3396384_XV, SRR3396385_XV, SRR3396386_XV, SRR3396387_XV" (✔) : 'independent.variable' : 'state' is in the column of phenodata.csv. ▶ Checking whether 'state' is a two-group 'independent.variable' ... (✔) : Column 'independent.variable' : 'state' of phenodata.csv is valid. ● 'independent.variable' : 'state' ************** Checking hierarchy of '/home/biocbuild/bbs-3.16-bioc/R/site-library/RNASeqRData/extdata/input_files/' ************ (✔) : 'Saccharomyces_cerevisiae_XV_Ensembl.gtf' is in 'input_files' (✔) : 'Saccharomyces_cerevisiae_XV_Ensembl.fa' is in 'input_files' (✔) : 'raw_fastq.gz/' is in 'input_files' (✔) : 'raw_fastq.gz/SRR3396381_XV_1.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396381_XV_2.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396382_XV_1.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396382_XV_2.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396384_XV_1.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396384_XV_2.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396385_XV_1.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396385_XV_2.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396386_XV_1.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396386_XV_2.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396387_XV_1.fastq.gz' is in 'input_files/' (✔) : 'raw_fastq.gz/SRR3396387_XV_2.fastq.gz' is in 'input_files/' (✔) : 'phenodata.csv is in 'input_files' (⚠) : 'indices/' is optional. You can download the corresponding 'XXX.ht2' from 'https://ccb.jhu.edu/software/hisat2/index.shtml' to speed up the process. (✔) : '/home/biocbuild/bbs-3.16-bioc/R/site-library/RNASeqRData/extdata/input_files/' is valid ! ************** Checking 'case.group' & 'control.group' ************ (✘) : 'case.group' : '60mins_ID20_amphotericin_B' is not a group of in 'independent.variable'. Error in CheckCaseControlGroup(input.path.prefix, independent.variable, : 'case.group' invalid ERROR Calls: RNASeqRParam -> CheckCaseControlGroup Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘RNASeqR.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/RNASeqR.Rcheck/00check.log’ for details.
RNASeqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL RNASeqR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘RNASeqR’ ... ** using staged installation ** R ** data ** 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 Warning: Package 'RNASeqR' is deprecated and will be removed from Bioconductor version 3.17 ** testing if installed package can be loaded from final location Warning: Package 'RNASeqR' is deprecated and will be removed from Bioconductor version 3.17 ** testing if installed package keeps a record of temporary installation path * DONE (RNASeqR)
RNASeqR.Rcheck/RNASeqR-Ex.timings
name | user | system | elapsed | |
All_Steps_Interface | 0.003 | 0.000 | 0.003 | |
All_Steps_Interface_CMD | 0.001 | 0.000 | 0.001 | |
CheckToolAll | 0.001 | 0.000 | 0.001 | |
RNASeqDifferentialAnalysis | 0.001 | 0.000 | 0.001 | |
RNASeqDifferentialAnalysis_CMD | 0.001 | 0.000 | 0.001 | |
RNASeqEnvironmentSet | 0.000 | 0.000 | 0.001 | |
RNASeqEnvironmentSet_CMD | 0.000 | 0.001 | 0.000 | |
RNASeqGoKegg | 0.000 | 0.001 | 0.000 | |
RNASeqGoKegg_CMD | 0.000 | 0.001 | 0.001 | |
RNASeqQualityAssessment | 0.001 | 0.000 | 0.001 | |
RNASeqQualityAssessment_CMD | 0.001 | 0.000 | 0.001 | |
RNASeqRParam-class | 0.001 | 0.000 | 0.001 | |