Philippe Hupe
| Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/GLAD |
| git_branch: devel |
| git_last_commit: 4e4241d |
| git_last_commit_date: 2023-10-24 09:34:02 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-04-29 11:40:52 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 875/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GLAD 2.67.0 (landing page) Philippe Hupe
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GLAD |
| Version: 2.67.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GLAD.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GLAD_2.67.0.tar.gz |
| StartedAt: 2024-04-29 06:37:15 -0000 (Mon, 29 Apr 2024) |
| EndedAt: 2024-04-29 06:37:46 -0000 (Mon, 29 Apr 2024) |
| EllapsedTime: 31.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GLAD.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GLAD.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GLAD_2.67.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GLAD.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.67.0’
* 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 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 ... 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: (-1) daglad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:196-199: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:202-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:207-210: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:213-216: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:218: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:221-224: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:226-228: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:240: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:241: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:242-243: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:244: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:245: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:246: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:247-248: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:249: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (5) glad.Rd:152: \item in \value must have non-empty label
checkRd: (-1) glad.Rd:159-160: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:162-165: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:168-171: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:173-176: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:178-179: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:182-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:189-190: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:195-196: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:213: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:214: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glad.Rd:225: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glad.Rd:226: Lost braces in \itemize; meant \describe ?
* 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-beta-2024-04-15_r86425/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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/GLAD.Rcheck/00check.log’
for details.
GLAD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL GLAD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c BkpInfo.cpp -o BkpInfo.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c HaarSeg.cpp -o HaarSeg.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c MoveBkp.cpp -o MoveBkp.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c OutliersGNL.cpp -o OutliersGNL.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c chrBreakpoints.cpp -o chrBreakpoints.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c cutree.cpp -o cutree.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c daglad.cpp -o daglad.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c distance.cpp -o distance.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c filterBkp.cpp -o filterBkp.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c findCluster.cpp -o findCluster.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c glad-utils.cpp -o glad-utils.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c hclust.cpp -o hclust.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c laws.c -o laws.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -fPIC -g -O2 -Wall -c loopRemove.cpp -o loopRemove.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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 | 0.000 | 0.000 | 0.001 | |
| ColorBar | 0.028 | 0.000 | 0.028 | |
| arrayCGH | 0.039 | 0.000 | 0.040 | |
| arrayPersp | 0 | 0 | 0 | |
| arrayPlot | 0.069 | 0.000 | 0.068 | |
| as.data.frame.profileCGH | 0.226 | 0.016 | 0.242 | |
| as.profileCGH | 0.056 | 0.000 | 0.055 | |
| bladder | 0.018 | 0.000 | 0.018 | |
| cytoband | 0.006 | 0.004 | 0.009 | |
| daglad | 0.356 | 0.012 | 0.368 | |
| glad | 0.416 | 0.004 | 0.421 | |
| hclust | 0.021 | 0.000 | 0.022 | |
| myPalette | 0.007 | 0.000 | 0.006 | |
| plotProfile | 0.525 | 0.000 | 0.526 | |
| profileCGH | 0.06 | 0.00 | 0.06 | |
| snijders | 0.055 | 0.000 | 0.056 | |
| veltman | 0.030 | 0.016 | 0.045 | |