Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 1177/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metahdep 1.58.0 (landing page) John R. Stevens
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the metahdep package: - 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: metahdep |
Version: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metahdep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metahdep_1.58.0.tar.gz |
StartedAt: 2023-10-18 06:01:58 -0400 (Wed, 18 Oct 2023) |
EndedAt: 2023-10-18 06:02:52 -0400 (Wed, 18 Oct 2023) |
EllapsedTime: 54.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: metahdep.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metahdep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metahdep_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/metahdep.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metahdep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metahdep’ version ‘1.58.0’ * 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 ‘metahdep’ can be installed ... WARNING Found the following significant warnings: metahdep.c:471:79: warning: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion] See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/metahdep.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 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 dependencies in R code ... NOTE 'library' or 'require' call to ‘affyPLM’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘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 ... OK * checking R code for possible problems ... NOTE LinMod.HBLM.fast.dep: no visible global function definition for ‘pnorm’ LinMod.MetAn.dep.FEMA: no visible global function definition for ‘pchisq’ LinMod.MetAn.dep.FEMA: no visible global function definition for ‘pt’ LinMod.MetAn.dep.REMA: no visible global function definition for ‘pchisq’ LinMod.MetAn.dep.REMA: no visible global function definition for ‘pt’ LinMod.REMA.delta.split: no visible global function definition for ‘pt’ LinMod.REMA.delta.split: no visible global function definition for ‘pchisq’ getPLM.es: no visible global function definition for ‘fitPLM’ getPLM.es: no visible global function definition for ‘coefs’ getPLM.es: no visible global function definition for ‘varcov’ getPLM.es: no visible global function definition for ‘new’ getPLM.es: no visible global function definition for ‘annotation’ metahdep: no visible global function definition for ‘flush.console’ metahdep.FEMA: no visible global function definition for ‘pchisq’ metahdep.FEMA: no visible global function definition for ‘pnorm’ metahdep.HBLM: no visible global function definition for ‘new’ metahdep.REMA: no visible global function definition for ‘new’ metahdep.format: no visible global function definition for ‘sd’ metahdep.format: no visible global function definition for ‘flush.console’ metahdep.format: no visible global function definition for ‘new’ new.LinMod.HBLM.fast.dep.delta.split: no visible global function definition for ‘pnorm’ Undefined global functions or variables: annotation coefs fitPLM flush.console new pchisq pnorm pt sd varcov Consider adding importFrom("methods", "new") importFrom("stats", "pchisq", "pnorm", "pt", "sd") importFrom("utils", "flush.console") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: metahdep.other.Rd:40-42: Dropping empty section \usage prepare_Rd: metahdep.other.Rd:43-45: Dropping empty section \arguments prepare_Rd: metahdep.other.Rd:46-48: Dropping empty section \value * 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 C/C++/Fortran sources/headers ... 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 in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/meat/metahdep.Rcheck/00check.log’ for details.
metahdep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metahdep ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘metahdep’ ... ** 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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c metahdep.c -o metahdep.o metahdep.c:471:79: warning: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion] index = metan_binary_search_unique(name_list, sort_index, R_old_names, j, CHAR(STRING_ELT(R_old_chipsets, j)), i); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:197:17: note: expanded from macro 'CHAR' #define CHAR(x) R_CHAR(x) ^~~~~~~~~ metahdep.c:372:103: note: passing argument to parameter 'chipset_name' here SEXP metan_binary_search_unique(SEXP name_list, SEXP sort_index, SEXP gene_name, int gene_index, char chipset_name, int study_num) ^ 1 warning generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o metahdep.so metahdep.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-metahdep/00new/metahdep/libs ** R ** data ** 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 (metahdep)
metahdep.Rcheck/metahdep-Ex.timings
name | user | system | elapsed | |
ES.obj-class | 0.027 | 0.006 | 0.051 | |
HGU.DifExp.list | 0.009 | 0.002 | 0.015 | |
HGU.newnames | 0.062 | 0.005 | 0.103 | |
HGU.prep.list | 0.044 | 0.006 | 0.076 | |
getPLM.es | 0.001 | 0.000 | 0.000 | |
gloss | 0.003 | 0.002 | 0.005 | |
metahdep.FEMA | 0.028 | 0.006 | 0.054 | |
metahdep.HBLM | 0.497 | 0.017 | 0.793 | |
metahdep | 1.081 | 0.032 | 1.709 | |
metahdep.REMA | 0.036 | 0.006 | 0.058 | |
metahdep.format | 0.159 | 0.011 | 0.245 | |
metahdep.other | 0.001 | 0.001 | 0.004 | |
metaprep-class | 0.036 | 0.005 | 0.067 | |