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This page was generated on 2024-05-22 11:34:48 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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 689/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomePeak2 1.16.0  (landing page)
Zhen Wei
Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024)
git_url: https://git.bioconductor.org/packages/exomePeak2
git_branch: RELEASE_3_19
git_last_commit: dac530f
git_last_commit_date: 2024-04-30 11:21:17 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for exomePeak2 on nebbiolo1


To the developers/maintainers of the exomePeak2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/exomePeak2.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.

raw results


Summary

Package: exomePeak2
Version: 1.16.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings exomePeak2_1.16.0.tar.gz
StartedAt: 2024-05-21 22:35:44 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 22:40:40 -0400 (Tue, 21 May 2024)
EllapsedTime: 296.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: exomePeak2.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings exomePeak2_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/exomePeak2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘exomePeak2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomePeak2’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘exomePeak2’ 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 whether startup messages can be suppressed ... 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
plotGCbias: no visible binding for global variable ‘glmFit’
plotGCbias: no visible binding for global variable ‘IP_input’
plotGCbias: no visible binding for global variable ‘Perturbation’
Undefined global functions or variables:
  IP_input Perturbation glmFit
* 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 ... ERROR
Running examples in ‘exomePeak2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exomePeak2
> ### Title: Peak Calling and Differential Analysis of MeRIP-seq.
> ### Aliases: exomePeak2
> 
> ### ** Examples
> 
> 
> ## Specify File Directories
> GENE_ANNO_GTF = system.file("extdata", "example.gtf", package="exomePeak2")
> 
> f1 = system.file("extdata", "IP1.bam", package="exomePeak2")
> f2 = system.file("extdata", "IP2.bam", package="exomePeak2")
> f3 = system.file("extdata", "IP3.bam", package="exomePeak2")
> f4 = system.file("extdata", "IP4.bam", package="exomePeak2")
> IP_BAM = c(f1,f2,f3,f4)
> f1 = system.file("extdata", "Input1.bam", package="exomePeak2")
> f2 = system.file("extdata", "Input2.bam", package="exomePeak2")
> f3 = system.file("extdata", "Input3.bam", package="exomePeak2")
> INPUT_BAM = c(f1,f2,f3)
> 
> ## Peak Calling
> res <- exomePeak2(bam_ip = IP_BAM,
+                   bam_input = INPUT_BAM,
+                   gff = GENE_ANNO_GTF,
+                   genome = "hg19")
Error in load_package_gracefully("txdbmaker", "starting with BioC 3.19, ",  : 
  Could not load package txdbmaker. Is it installed?

  Note that starting with BioC 3.19, calling makeTxDbFromGFF() requires
  the txdbmaker package. Please install it with:

    BiocManager::install("txdbmaker")
Calls: exomePeak2 ... makeTxDbFromGFF -> call_fun_in_txdbmaker -> load_package_gracefully
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_V_2.00.Rmd’ using rmarkdown

Quitting from lines 50-71 [unnamed-chunk-2] (Vignette_V_2.00.Rmd)
Error: processing vignette 'Vignette_V_2.00.Rmd' failed with diagnostics:
Could not load package txdbmaker. Is it installed?

  Note that starting with BioC 3.19, calling makeTxDbFromGFF() requires
  the txdbmaker package. Please install it with:

    BiocManager::install("txdbmaker")
--- failed re-building ‘Vignette_V_2.00.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette_V_2.00.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/exomePeak2.Rcheck/00check.log’
for details.


Installation output

exomePeak2.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL exomePeak2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘exomePeak2’ ...
** 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
Warning in fun(libname, pkgname) :
  Package 'exomePeak2' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'exomePeak2' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (exomePeak2)

Tests output


Example timings

exomePeak2.Rcheck/exomePeak2-Ex.timings

nameusersystemelapsed