| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:33:42 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| 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 | ||||
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To the developers/maintainers of the crlmm package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crlmm.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 436/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| crlmm 1.57.0 (landing page) Benilton S Carvalho
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: crlmm |
| Version: 1.57.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:crlmm.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings crlmm_1.57.0.tar.gz |
| StartedAt: 2023-01-28 20:47:22 -0000 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 20:55:34 -0000 (Sat, 28 Jan 2023) |
| EllapsedTime: 492.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: crlmm.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:crlmm.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings crlmm_1.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/crlmm.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘crlmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crlmm’ version ‘1.57.0’
* 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 ‘crlmm’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'crlmm' was found
* 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 ... WARNING
Error in library(crlmm, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘crlmm’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘splines’
All declared Imports should be used.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
calculateRBafCNSet : processByChromosome: no visible global function
definition for ‘position’
genotypeInf: no visible binding for global variable ‘anno’
krlmm: no visible binding for global variable ‘VGLMparameters’
Undefined global functions or variables:
VGLMparameters anno defineTestSuite position printTextProtocol
runTestSuite
* checking Rd files ... WARNING
checkRd: (5) CNSet-methods.Rd:39-41: \item in \describe must have non-empty label
checkRd: (5) CNSet-methods.Rd:65-67: \item in \describe must have non-empty label
checkRd: (5) CNSet-methods.Rd:69-71: \item in \describe must have non-empty label
checkRd: (-1) constructInf.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) genotype.Illumina.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:39: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:55: Escaped LaTeX specials: \_ \_
checkRd: (-1) readIdatFiles.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) snprma.Rd:38: 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘crlmm_unit_tests.R’
ERROR
Running the tests in ‘tests/crlmm_unit_tests.R’ failed.
Last 13 lines of output:
Processing 3 files.
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|======================= | 33%
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|=============================================== | 67%
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|======================================================================| 100%
Loading annotations.
Determining gender.
Calling 906600 SNPs for recalibration... Done.
Estimating recalibration parameters.
Calling 906600 SNPs... Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘AffyGW.Rnw’... OK
‘CopyNumberOverview.Rnw’... OK
‘IlluminaPreprocessCN.Rnw’... OK
‘Infrastructure.Rnw’... OK
‘genotyping.Rnw’... failed to complete the test
‘gtypeDownstream.Rnw’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘genotyping.Rnw’
...
> path <- system.file("celFiles", package = "hapmapsnp6")
> celFiles <- list.celfiles(path, full.names = TRUE)
> system.time(crlmmResult <- crlmm(celFiles, verbose = FALSE))
Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Killed
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 3 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/crlmm.Rcheck/00check.log’
for details.
crlmm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL crlmm ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘crlmm’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-crlmm/00new/crlmm/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** testing if installed package keeps a record of temporary installation path * DONE (crlmm)
crlmm.Rcheck/tests/crlmm_unit_tests.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "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.
> require("crlmm") || stop("unable to load crlmm package")
Loading required package: crlmm
Loading required package: oligoClasses
Welcome to oligoClasses version 1.61.0
Loading required package: preprocessCore
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to crlmm version 1.57.0
[1] TRUE
> crlmm:::.test()
Loading required package: genomewidesnp6Crlmm
Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Loading required package: hapmapsnp6
/-------------------------------------------\
| SAMPLE HAPMAP SNP 6.0 |
|-------------------------------------------|
| Data obtained from http://www.hapmap.org |
| This package is meant to be used only for |
| demonstration of BioConductor packages. |
| Access http://www.hapmap.org for details. |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy. |
\-------------------------------------------/
Loading annotations and mixture model parameters.
Processing 3 files.
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| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Loading annotations.
Determining gender.
Calling 906600 SNPs for recalibration... Done.
Estimating recalibration parameters.
Calling 906600 SNPs... Killed