Andreas Mitterecker
| Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/fabia |
| git_branch: devel |
| git_last_commit: c680892 |
| git_last_commit_date: 2024-10-29 09:34:18 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:41 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
| 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 684/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fabia 2.53.0 (landing page) Andreas Mitterecker
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the fabia package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fabia.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. |
| Package: fabia |
| Version: 2.53.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fabia.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings fabia_2.53.0.tar.gz |
| StartedAt: 2024-12-23 00:38:04 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 00:39:05 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 60.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: fabia.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fabia.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings fabia_2.53.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/fabia.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '2.53.0'
* 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 whether package 'fabia' can be installed ... OK
* 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 whether startup messages can be suppressed ... 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
File 'fabia/R/zzz.R':
.onLoad calls:
packageStartupMessage("+----------------------------+ \n", "|............................| \n", "|............................| \n", "|..............########......| ####### # ###### ### # \n", "|..............########......| # # # # # # # # \n", "|.....####.....########......| # # # # # # # # \n", "|.....####.....########......| ##### # # ###### # # # \n", "|.....####...................| # ####### # # # ####### \n", "|.....####...........###.....| # # # # # # # # \n", "|....................###.....| # # # ###### ### # # \n", "|....................###.....| \n", "|............................| \n", "+----------------------------+ \n")
packageStartupMessage("Citation: S. Hochreiter et al.,", "\n", "FABIA: Factor Analysis for Bicluster Acquisition,", "\n", "Bioinformatics 26(12):1520-1527, 2010.", "\n", "BibTex: enter 'toBibtex(citation(\"fabia\"))'", "\n\n", "Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html", "\n\n", "FABIA Package Version ", version, "\n")
See section 'Good practice' in '?.onAttach'.
plot,Factorization-missing: warning in symbols(ll[isel, 1], ll[isel,
2], circle = sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg =
colors[2]): partial argument match of 'circle' to 'circles'
plot,Factorization-missing: warning in symbols(zz[ii, 1], zz[ii, 2],
square = sqs, inches = FALSE, lwd = 3, add = TRUE, fg = colors[2 +
iGroup[i]]): partial argument match of 'square' to 'squares'
.onLoad: no visible global function definition for 'winMenuNames'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
plot,Factorization-missing: no visible global function definition for
'dev.new'
Undefined global functions or variables:
dev.new winMenuAdd winMenuAddItem winMenuNames
Consider adding
importFrom("grDevices", "dev.new")
importFrom("utils", "winMenuAdd", "winMenuAddItem", "winMenuNames")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) Factorization-class.Rd:346: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:398: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:401: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:402: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:408: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:409: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:410: \item in \arguments must have non-empty label
checkRd: (-1) Factorization-class.Rd:511: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:512: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:513: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:514: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:529: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:530: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:531: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:532: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:548: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:550: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:552: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:554: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:556: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:558: Lost braces in \enumerate; meant \describe ?
checkRd: (5) Factorization-class.Rd:416: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:417-418: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:419: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:424: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:425: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:426: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:427: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:428: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:429: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:167-177: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:179-183: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:185-189: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:191-196: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:198-203: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:205-210: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:212-217: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:219-224: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:226-231: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:233-238: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:240-245: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:247-252: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:254-259: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:261-267: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:269-275: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:277-283: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:285-290: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:292-298: \item in \describe must have non-empty label
checkRd: (-1) Factorization-class.Rd:331: Lost braces
331 | \item{plot}{\code{signature(x = "Factorization", y = "missing")}}{ Plot of a matrix factorization result}
| ^
checkRd: (-1) Factorization-class.Rd:333: Lost braces
333 | \item{show}{\code{signature(object = "Factorization")}}{ Display statistics of a matrix factorization result}
| ^
checkRd: (-1) Factorization-class.Rd:336-337: Lost braces
336 | "numeric")}}{ Display
| ^
checkRd: (-1) Factorization-class.Rd:339: Lost braces
339 | \item{summary}{\code{signature(object = "Factorization")}}{ Summary of matrix factorization result}
| ^
checkRd: (5) fabi.Rd:66-82: \item in \value must have non-empty label
checkRd: (5) fabia.Rd:75-91: \item in \value must have non-empty label
checkRd: (5) fabiap.Rd:88-104: \item in \value must have non-empty label
checkRd: (5) fabias.Rd:77-93: \item in \value must have non-empty label
checkRd: (5) fabiasp.Rd:65-81: \item in \value must have non-empty label
checkRd: (5) mfsc.Rd:75-83: \item in \value must have non-empty label
checkRd: (5) nmfdiv.Rd:49-55: \item in \value must have non-empty label
checkRd: (5) nmfeu.Rd:50-56: \item in \value must have non-empty label
checkRd: (5) nmfsc.Rd:76-82: \item in \value must have non-empty label
checkRd: (5) readSpfabiaResult.Rd:24-35: \item in \value must have non-empty label
checkRd: (5) samplesPerFeature.Rd:46-51: \item in \value must have non-empty label
checkRd: (-1) samplesPerFeature.Rd:49-50: Lost braces
49 | \code{nsL} {Vector of feature length containing number of samples
| ^
checkRd: (5) spfabia.Rd:113-124: \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 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 include directives in Makefiles ... NOTE
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives. However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME. This option can be specified
multiple times to include multiple Makefiles. Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/fabia/libs/x64/fabia.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'fabia.pdf' from 692Kb to 548Kb
consider running tools::compactPDF() on these files,
or build the source package with --compact-vignettes
* 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: 1 WARNING, 4 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/fabia.Rcheck/00check.log'
for details.
fabia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL fabia ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'fabia' ... ** using staged installation ** libs running 'src/Makefile.win' ... E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:290: warning: overriding recipe for target '.c.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:290: warning: ignoring old recipe for target '.c.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:292: warning: overriding recipe for target '.c.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:292: warning: ignoring old recipe for target '.c.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:295: warning: overriding recipe for target '.cc.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:295: warning: ignoring old recipe for target '.cc.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:297: warning: overriding recipe for target '.cpp.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:297: warning: ignoring old recipe for target '.cpp.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:299: warning: overriding recipe for target '.cc.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:299: warning: ignoring old recipe for target '.cc.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:302: warning: overriding recipe for target '.cpp.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:302: warning: ignoring old recipe for target '.cpp.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:305: warning: overriding recipe for target '.m.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:305: warning: ignoring old recipe for target '.m.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:307: warning: overriding recipe for target '.m.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:307: warning: ignoring old recipe for target '.m.d' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:310: warning: overriding recipe for target '.mm.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:310: warning: ignoring old recipe for target '.mm.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:312: warning: overriding recipe for target '.M.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:312: warning: ignoring old recipe for target '.M.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:314: warning: overriding recipe for target '.f.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:314: warning: ignoring old recipe for target '.f.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:316: warning: overriding recipe for target '.f95.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:316: warning: ignoring old recipe for target '.f95.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:318: warning: overriding recipe for target '.f90.o' E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:318: warning: ignoring old recipe for target '.f90.o' rm -f fabia.o fabia.dll *.a *.o *.so *.dll gcc -c fabiac.c -o fabia.o -I"E:/biocbuild/bbs-3.21-bioc/R/include" -Wall -O3 gcc -shared -s -static-libgcc fabia.o -L"E:/biocbuild/bbs-3.21-bioc/R/bin/x64" -lR -o fabia.dll rm -f fabia.o *.a *.o *.so installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-fabia/00new/fabia/libs/x64 ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fabia)
fabia.Rcheck/fabia-Ex.timings
| name | user | system | elapsed | |
| Factorization-class | 0.86 | 0.00 | 0.86 | |
| estimateMode | 0 | 0 | 0 | |
| extractBic | 0.06 | 0.00 | 0.07 | |
| extractPlot | 0.19 | 0.02 | 0.20 | |
| fabi | 0.04 | 0.05 | 0.09 | |
| fabia | 0.05 | 0.01 | 0.07 | |
| fabiaDemo | 0 | 0 | 0 | |
| fabiaVersion | 0 | 0 | 0 | |
| fabiap | 0.03 | 0.02 | 0.04 | |
| fabias | 0.07 | 0.00 | 0.07 | |
| fabiasp | 0.33 | 0.06 | 0.39 | |
| makeFabiaData | 0.12 | 0.00 | 0.13 | |
| makeFabiaDataBlocks | 0.08 | 0.02 | 0.09 | |
| makeFabiaDataBlocksPos | 0.10 | 0.00 | 0.09 | |
| makeFabiaDataPos | 0.06 | 0.01 | 0.08 | |
| matrixImagePlot | 0.06 | 0.00 | 0.06 | |
| mfsc | 0.11 | 0.02 | 0.13 | |
| nmfdiv | 0.09 | 0.00 | 0.09 | |
| nmfeu | 0.08 | 0.00 | 0.08 | |
| nmfsc | 0.05 | 0.05 | 0.10 | |
| plotBicluster | 0.11 | 0.00 | 0.10 | |
| projFunc | 0 | 0 | 0 | |
| projFuncPos | 0 | 0 | 0 | |
| readSamplesSpfabia | 0 | 0 | 0 | |
| samplesPerFeature | 0 | 0 | 0 | |
| spfabia | 0.06 | 0.01 | 0.10 | |