Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 964/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HilbertVis 1.64.0 (landing page) Simon Anders
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the HilbertVis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HilbertVis.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: HilbertVis |
Version: 1.64.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HilbertVis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HilbertVis_1.64.0.tar.gz |
StartedAt: 2024-11-19 22:59:34 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:07:28 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 474.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HilbertVis.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HilbertVis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HilbertVis_1.64.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/HilbertVis.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HilbertVis/DESCRIPTION’ ... OK * this is package ‘HilbertVis’ version ‘1.64.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘HilbertVis’ can be installed ... WARNING Found the following significant warnings: make_wiggle_vector.c:16:17: warning: format string is not a string literal (potentially insecure) [-Wformat-security] shrink_vector.c:76:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] shrink_vector.c:76:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/HilbertVis.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 dependencies in R code ... NOTE 'library' or 'require' call to ‘EBImage’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE makeRandomTestData: no visible global function definition for ‘runif’ makeRandomTestData: no visible global function definition for ‘rgamma’ makeRandomTestData: no visible global function definition for ‘dnorm’ makeRandomTestData: no visible global function definition for ‘rpois’ plotLongVector: no visible global function definition for ‘segments’ showHilbertImage: no visible global function definition for ‘colorRampPalette’ showHilbertImage: no visible global function definition for ‘col2rgb’ showHilbertImage: no visible global function definition for ‘flip’ showHilbertImage: no visible global function definition for ‘rgbImage’ showHilbertImage: no visible global function definition for ‘Image’ showHilbertImage: no visible global function definition for ‘display’ shrinkRleVector: no visible global function definition for ‘aggregate’ shrinkVector: no visible global function definition for ‘is’ Undefined global functions or variables: Image aggregate col2rgb colorRampPalette display dnorm flip is rgamma rgbImage rpois runif segments Consider adding importFrom("grDevices", "col2rgb", "colorRampPalette") importFrom("graphics", "segments") importFrom("methods", "is") importFrom("stats", "aggregate", "dnorm", "rgamma", "rpois", "runif") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘HilbertVisGUI’ * 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 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 ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/HilbertVis.Rcheck/00check.log’ for details.
HilbertVis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HilbertVis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘HilbertVis’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hilbert.c -o hilbert.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c make_wiggle_vector.c -o make_wiggle_vector.o make_wiggle_vector.c:16:17: warning: format string is not a string literal (potentially insecure) [-Wformat-security] error( buf ); ^~~ make_wiggle_vector.c:16:17: note: treat the string as an argument to avoid this error( buf ); ^ "%s", 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c shrink_vector.c -o shrink_vector.o shrink_vector.c:76:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if( abs( REAL( vector )[ j ] ) > abs( val ) ) ^ shrink_vector.c:76:20: note: use function 'fabs' instead if( abs( REAL( vector )[ j ] ) > abs( val ) ) ^~~ fabs shrink_vector.c:76:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] if( abs( REAL( vector )[ j ] ) > abs( val ) ) ^ shrink_vector.c:76:49: note: use function 'fabs' instead if( abs( REAL( vector )[ j ] ) > abs( val ) ) ^~~ fabs 2 warnings generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o HilbertVis.so hilbert.o make_wiggle_vector.o shrink_vector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-HilbertVis/00new/HilbertVis/libs ** R ** 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 (HilbertVis)
HilbertVis.Rcheck/HilbertVis-Ex.timings
name | user | system | elapsed | |
hilbertCurve | 0.005 | 0.004 | 0.009 | |
hilbertImage | 1.340 | 0.137 | 1.490 | |
makeRandomTestData | 0 | 0 | 0 | |
makeWiggleVector | 0.005 | 0.000 | 0.005 | |
plotHilbertCurve | 0.162 | 0.013 | 0.176 | |
plotLongVector | 0.117 | 0.011 | 0.129 | |
showHilbertImage | 0 | 0 | 0 | |
shrinkVector | 0.001 | 0.000 | 0.001 | |