| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:32 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 GLAD package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GLAD.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 832/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GLAD 2.65.0 (landing page) Philippe Hupe
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: GLAD |
| Version: 2.65.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GLAD.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GLAD_2.65.0.tar.gz |
| StartedAt: 2023-06-05 23:22:13 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 23:23:44 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GLAD.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GLAD.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GLAD_2.65.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GLAD.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.65.0’
* 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 ‘GLAD’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
Missing or unexported object: ‘aws::laws’
* 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 ... WARNING
checkRd: (5) as.profileCGH.Rd:25: \item in \value must have non-empty label
checkRd: (-1) daglad.Rd:47: Escaped LaTeX specials: \$
checkRd: (5) daglad.Rd:182-183: \item in \value must have non-empty label
checkRd: (5) glad.Rd:152: \item in \value must have non-empty label
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.0/site-library/GLAD/libs/GLAD.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘printf’, possibly from ‘printf’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘GLAD.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/GLAD.Rcheck/00check.log’
for details.
GLAD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL GLAD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘GLAD’ ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes GSL has been found on the operating system operating system: Linux configure: creating ./config.status config.status: creating src/Makevars src/Makevars file PKG_LIBS = -lgsl -lgslcblas -lm PKG_CPPFLAGS = -I/usr/local/include ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c BkpInfo.cpp -o BkpInfo.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c HaarSeg.cpp -o HaarSeg.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c MoveBkp.cpp -o MoveBkp.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c OutliersGNL.cpp -o OutliersGNL.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c chrBreakpoints.cpp -o chrBreakpoints.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c cutree.cpp -o cutree.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c daglad.cpp -o daglad.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c distance.cpp -o distance.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c filterBkp.cpp -o filterBkp.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c findCluster.cpp -o findCluster.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c glad-utils.cpp -o glad-utils.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c hclust.cpp -o hclust.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c laws.c -o laws.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -c loopRemove.cpp -o loopRemove.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -lgsl -lgslcblas -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-GLAD/00new/GLAD/libs ** R ** data ** demo ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GLAD)
GLAD.Rcheck/GLAD-Ex.timings
| name | user | system | elapsed | |
| ChrNumeric | 0 | 0 | 0 | |
| ColorBar | 0.023 | 0.004 | 0.027 | |
| arrayCGH | 0.030 | 0.008 | 0.038 | |
| arrayPersp | 0.000 | 0.000 | 0.001 | |
| arrayPlot | 0.066 | 0.000 | 0.066 | |
| as.data.frame.profileCGH | 0.225 | 0.004 | 0.229 | |
| as.profileCGH | 0.054 | 0.000 | 0.054 | |
| bladder | 0.017 | 0.000 | 0.018 | |
| cytoband | 0.012 | 0.000 | 0.013 | |
| daglad | 0.350 | 0.004 | 0.355 | |
| glad | 0.395 | 0.000 | 0.396 | |
| hclust | 0.023 | 0.000 | 0.023 | |
| myPalette | 0.006 | 0.000 | 0.006 | |
| plotProfile | 0.501 | 0.000 | 0.503 | |
| profileCGH | 0.051 | 0.004 | 0.055 | |
| snijders | 0.053 | 0.000 | 0.052 | |
| veltman | 0.024 | 0.036 | 0.060 | |