| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-27 05:50:29 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 BaalChIP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BaalChIP.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 114/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BaalChIP 1.25.0 (landing page) Ines de Santiago
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: BaalChIP |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BaalChIP_1.25.0.tar.gz |
| StartedAt: 2023-03-24 21:09:13 -0000 (Fri, 24 Mar 2023) |
| EndedAt: 2023-03-24 21:16:29 -0000 (Fri, 24 Mar 2023) |
| EllapsedTime: 435.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BaalChIP.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BaalChIP_1.25.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BaalChIP.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BaalChIP/DESCRIPTION’ ... OK
* this is package ‘BaalChIP’ version ‘1.25.0’
* 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 ‘BaalChIP’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 198.2Mb
sub-directories of 1Mb or more:
data 95.8Mb
test 101.9Mb
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
LazyData DB of 95.7 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BaalChIP-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BaalChIP.run
> ### Title: Method BaalChIP.run
> ### Aliases: BaalChIP.run BaalChIP.run,BaalChIP-method
>
> ### ** Examples
>
> samplesheet <- system.file("test", "exampleChIP.tsv", package = "BaalChIP")
> hets <- c("MCF7"= system.file("test", "MCF7_hetSNP.txt", package = "BaalChIP"),
+ "GM12891"= system.file("test", "GM12891_hetSNP.txt", package = "BaalChIP"))
> res <- BaalChIP(samplesheet=samplesheet, hets=hets)
-samplesheet checks: OK!
> res <- BaalChIP.run(res, cores=2)
-computing allele counts per BAM
|
| | 0%
|
|==== | 6%
|
|========= | 12%
|
|============= | 19%
|
|================== | 25%
|
|====================== | 31%
|
|========================== | 38%
|
|=============================== | 44%
|
|=================================== | 50%
|
|======================================= | 56%
|
|============================================ | 62%
|
|================================================ | 69%
|
|==================================================== | 75%
|
|========================================================= | 81%
|
|============================================================= | 88%
|
|================================================================== | 94%
|
|======================================================================| 100%
-applying filters per BAM
|
| | 0%
|
|==== | 6%
|
|========= | 12%
|
|============= | 19%
|
|================== | 25%
|
|====================== | 31%
|
|========================== | 38%
|
|=============================== | 44%
|
|=================================== | 50%
|
|======================================= | 56%
|
|============================================ | 62%
|
|================================================ | 69%
|
|==================================================== | 75%
|
|========================================================= | 81%
|
|============================================================= | 88%
|
|================================================================== | 94%
|
|======================================================================| 100%
-merging replicated samples...
-filtering out SNPs with only 1 observed allele...
-QC complete!
-geting ASB counts...
will use RAF values for MCF7 group from hets file
will use RAF values for GM12891 group from hets file
... calculating ASB for: MCF7
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘BaalChIP.Rmd’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘BaalChIP.Rmd’ using rmarkdown
Killed
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BaalChIP.Rcheck/00check.log’
for details.
BaalChIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BaalChIP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘BaalChIP’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (BaalChIP)
BaalChIP.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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.
> BiocGenerics:::testPackage("BaalChIP")
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Fri Mar 24 21:15:24 2023
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
BaalChIP 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
10.820 0.480 11.451
BaalChIP.Rcheck/BaalChIP-Ex.timings
| name | user | system | elapsed | |
| BaalChIP | 0.036 | 0.001 | 0.038 | |
| BaalChIP.get | 0.115 | 0.003 | 0.122 | |
| BaalChIP.report | 0.022 | 0.000 | 0.021 | |