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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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Package 406/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.39.0  (landing page)
Tiphaine Martin
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/coMET
git_branch: devel
git_last_commit: 0dcb6aa
git_last_commit_date: 2024-10-29 11:16:09 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for coMET on kjohnson3

To the developers/maintainers of the coMET package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coMET.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: coMET
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.39.0.tar.gz
StartedAt: 2024-12-23 18:42:22 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 18:46:00 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 217.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: coMET.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.39.0’
* 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 ‘coMET’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 18.9Mb
  sub-directories of 1Mb or more:
    data      7.6Mb
    extdata  10.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
draw.plot.annotation : <anonymous>: no visible global function
  definition for 'ggplotGrob'
draw.plot.annotation: no visible global function definition for
  'viewTracks'
draw.plot.annotation: no visible global function definition for
  'trackList'
eQTL: no visible binding for global variable 'chromosome_stop'
eQTL: no visible binding for global variable 'chromosome_start'
eQTL: no visible binding for global variable 'chromosome_name'
eQTL_GTEx: no visible binding for global variable 'snp_pos'
eQTL_GTEx: no visible binding for global variable 'snp_chrom'
eQTL_GTEx: no visible binding for global variable 'gene_start'
eQTL_GTEx: no visible binding for global variable 'gene_stop'
eQTL_GTEx: no visible binding for global variable 'gene_chr'
geneExpression_GTEx: no visible global function definition for 'as'
metQTL: no visible binding for global variable 'chromosome_stop'
metQTL: no visible binding for global variable 'chromosome_start'
metQTL: no visible binding for global variable 'chromosome_name'
pizza: no visible global function definition for 'par'
pizza: no visible global function definition for 'plot.new'
pizza: no visible global function definition for 'plot.window'
pizza: no visible global function definition for 'polygon'
pizza: no visible global function definition for 'lines'
pizza: no visible global function definition for 'text'
psiQTL_GTEx: no visible binding for global variable 'pos_snp'
psiQTL_GTEx: no visible binding for global variable 'chr_snp'
psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon'
psiQTL_GTEx: no visible binding for global variable 'chr_exon'
Undefined global functions or variables:
  as chr_exon chr_snp chromosome_name chromosome_start chromosome_stop
  gene_chr gene_start gene_stop ggplotGrob lines par plot.new
  plot.window polygon pos_middle_exon pos_snp snp_chrom snp_pos text
  trackList viewTracks
Consider adding
  importFrom("graphics", "lines", "par", "plot.new", "plot.window",
             "polygon", "text")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) ChIPTF_ENCODE.Rd:36: Escaped LaTeX specials: \#
* 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 ... NOTE
Objects in \usage without \alias in Rd file 'check.configVar.cometlist.Rd':
  ‘check.configVar.cometlist’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘coMET-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imprintedGenes_GTEx
> ### Title: Creates a imprinted genes track from GTEx
> ### Aliases: imprintedGenes_GTEx
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library("Gviz")
> gen<-"hg19"
> chr<- "chr6"
> start <- 144251437
> end <- 144330541
> 
> if(interactive()){
+    allIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="all", classification="imprinted",showId=TRUE)
+    allimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="all", classification="imprinted",showId=TRUE)
+    StomachIGtrack <-imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="Stomach", classification="all",showId=TRUE)
+    PancreasIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="Pancreas", classification="all",showId=TRUE)
+    PancreasimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
+    tissues="Pancreas", classification="biallelic",showId=TRUE)
+ 
+    imprintinglist <- list(allIGtrack,allimprintedIGtrack,
+    StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)
+ 
+   plotTracks(imprintinglist, from = start, to = end,
+                                    fontfamily="sans",fontfamily.title="sans")
+ 
+ } else {
+ 
+   data(allIGtrack)
+   data(allimprintedIGtrack)
+   data(StomachIGtrack)
+   data(PancreasIGtrack)
+   data(PancreasimprintedIGtrack)
+ 
+    imprintinglist <- list(allIGtrack,allimprintedIGtrack,
+    StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)
+ 
+   plotTracks(imprintinglist, from = start, to = end,
+                                    fontfamily="sans",fontfamily.title="sans")
+ }
Error in do.call(c, obj@http_config) : 
  no slot of name "http_config" for this object of class "Mart"
Calls: plotTracks ... list2 -> martHTTPConfig -> martHTTPConfig -> do.call
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
coMET-package 2.879  0.100  24.291
comet.web     2.431  0.131  17.455
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/coMET.Rcheck/00check.log’
for details.


Installation output

coMET.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL coMET
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘coMET’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
** testing if installed package keeps a record of temporary installation path
* DONE (coMET)

Tests output

coMET.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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.

> require("coMET") || stop("unable to load Package:coMET")
Loading required package: coMET
Loading required package: grid
Loading required package: biomaRt
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: psych

Attaching package: 'psych'

The following object is masked from 'package:GenomicRanges':

    distance

The following objects are masked from 'package:IRanges':

    distance, reflect

[1] TRUE
Warning message:
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' 
> BiocGenerics:::testPackage("coMET")


RUNIT TEST PROTOCOL -- Mon Dec 23 18:45:55 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
coMET RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  6.363   0.260   6.665 

Example timings

coMET.Rcheck/coMET-Ex.timings

nameusersystemelapsed
COSMIC_UCSC0.7830.0160.799
ChIPTF_ENCODE0.2210.0080.228
ClinVarCnv_UCSC0.1230.0120.135
ClinVarMain_UCSC0.1310.0020.134
CoreillCNV_UCSC0.1230.0010.126
DNAse_UCSC000
DNaseI_FANTOM0.2140.0130.228
DNaseI_RoadMap0.0840.0030.089
GAD_UCSC0.1190.0020.121
GWAScatalog_UCSC0.0990.0020.101
GeneReviews_UCSC0.1580.0010.159
HiCdata2matrix0.0100.0010.012
HistoneAll_UCSC1.2390.0031.243
HistoneOne_UCSC0.1150.0030.119
ISCA_UCSC0.1320.0020.134
TFBS_FANTOM0.1230.0020.125
bindingMotifsBiomart_ENSEMBL0.0460.0040.050
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.2040.0050.208
chromatinHMMAll_UCSC1.2640.0061.272
chromatinHMMOne_UCSC0.1410.0020.144
coMET-package 2.879 0.10024.291
col2HSV000
comet0.8610.0190.880
comet.list0.2080.0030.212
comet.web 2.431 0.13117.455
complementary0.0090.0000.009
cpgIslands_UCSC0.0440.0020.046
dgfootprints_RoadMap0.2500.0040.255
eQTL0.4260.0060.441
eQTL_GTEx0.4000.0040.404
gcContent_UCSC0.6270.0110.638
genesName_ENSEMBL0.0020.0010.003
genes_ENSEMBL0.2630.0020.280