Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:29 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 247/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BufferedMatrixMethods 1.66.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the BufferedMatrixMethods package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrixMethods.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: BufferedMatrixMethods |
Version: 1.66.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BufferedMatrixMethods.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BufferedMatrixMethods_1.66.0.tar.gz |
StartedAt: 2023-11-02 08:55:21 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 08:55:42 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 20.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BufferedMatrixMethods.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BufferedMatrixMethods.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BufferedMatrixMethods_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BufferedMatrixMethods.Rcheck’ * using R version 4.3.1 (2023-06-16) * 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 * using option ‘--no-vignettes’ * checking for file ‘BufferedMatrixMethods/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BufferedMatrixMethods’ version ‘1.66.0’ * 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 ‘BufferedMatrixMethods’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... OK * checking package 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 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 dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘affy’ ‘affyio’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘BufferedMatrix’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function calls to a different package: .Call("ReadHeader", ..., PACKAGE = "affyio") .Call("read_probeintensities", ..., PACKAGE = "affyio") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE NB: .First.lib is obsolete and will not be used in R >= 3.0.0 BufferedMatrix.bg.correct.normalize.quantiles: no visible global function definition for ‘is’ BufferedMatrix.bg.correct.normalize.quantiles: no visible global function definition for ‘duplicate’ BufferedMatrix.bg.correct.normalize.quantiles : bg.dens: no visible global function definition for ‘density’ BufferedMatrix.justRMA: no visible global function definition for ‘new’ BufferedMatrix.justRMA: no visible global function definition for ‘pData’ BufferedMatrix.justRMA: no visible global function definition for ‘read.celfile.header’ BufferedMatrix.justRMA: no visible global function definition for ‘cleancdfname’ BufferedMatrix.justRMA: no visible global function definition for ‘pmindex’ BufferedMatrix.justRMA: no visible global function definition for ‘geneNames’ BufferedMatrix.justRMA: no visible global function definition for ‘set.buffer.dim’ BufferedMatrix.justRMA: no visible global function definition for ‘RowMode’ BufferedMatrix.justRMA: no visible global function definition for ‘notes<-’ BufferedMatrix.read.celfiles: no visible global function definition for ‘createBufferedMatrix’ BufferedMatrix.read.celfiles: no visible global function definition for ‘read.celfile’ BufferedMatrix.read.celfiles: no visible global function definition for ‘AddColumn’ BufferedMatrix.read.probematrix: no visible global function definition for ‘new’ BufferedMatrix.read.probematrix: no visible global function definition for ‘cleancdfname’ BufferedMatrix.read.probematrix: no visible global function definition for ‘getCdfInfo’ BufferedMatrix.read.probematrix: no visible global function definition for ‘createBufferedMatrix’ BufferedMatrix.read.probematrix: no visible global function definition for ‘AddColumn’ bg.correct.BufferedMatrix: no visible global function definition for ‘is’ bg.correct.BufferedMatrix: no visible global function definition for ‘duplicate’ bg.correct.BufferedMatrix : bg.dens: no visible global function definition for ‘density’ normalize.BufferedMatrix.quantiles: no visible global function definition for ‘is’ normalize.BufferedMatrix.quantiles: no visible global function definition for ‘duplicate’ Undefined global functions or variables: AddColumn RowMode cleancdfname createBufferedMatrix density duplicate geneNames getCdfInfo is new notes<- pData pmindex read.celfile read.celfile.header set.buffer.dim Consider adding importFrom("methods", "is", "new") importFrom("stats", "density") 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 ... 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 C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking examples ... NONE * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log’ for details.
BufferedMatrixMethods.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BufferedMatrixMethods ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘BufferedMatrixMethods’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/BufferedMatrix/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init_package.c -o init_package.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/BufferedMatrix/include' -I/usr/local/include -fPIC -g -O2 -Wall -c preprocess_bm.c -o preprocess_bm.o preprocess_bm.c: In function ‘bm_rma_bg_correct’: preprocess_bm.c:344:7: warning: unused variable ‘i’ [-Wunused-variable] 344 | int i,j; | ^ preprocess_bm.c: In function ‘R_bm_rma_bg_correct’: preprocess_bm.c:378:7: warning: unused variable ‘current_mode’ [-Wunused-variable] 378 | int current_mode; | ^~~~~~~~~~~~ preprocess_bm.c: In function ‘R_bm_quantile_normalize’: preprocess_bm.c:593:7: warning: unused variable ‘current_mode’ [-Wunused-variable] 593 | int current_mode; | ^~~~~~~~~~~~ preprocess_bm.c: In function ‘do_RMA_buffmat’: preprocess_bm.c:924:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 924 | int first_ind; | ^~~~~~~~~ preprocess_bm.c: In function ‘R_bm_rma_bg_correct_quantile_normalize’: preprocess_bm.c:1151:7: warning: unused variable ‘current_mode’ [-Wunused-variable] 1151 | int current_mode; | ^~~~~~~~~~~~ At top level: preprocess_bm.c:453:12: warning: ‘min’ defined but not used [-Wunused-function] 453 | static int min(int x1,int x2){ | ^~~ gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o BufferedMatrixMethods.so init_package.o preprocess_bm.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-BufferedMatrixMethods/00new/BufferedMatrixMethods/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (BufferedMatrixMethods)