Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the bridge package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bridge.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 214/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bridge 1.56.0 (landing page) Raphael Gottardo
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: bridge |
Version: 1.56.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bridge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bridge_1.56.0.tar.gz |
StartedAt: 2021-10-14 16:56:51 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:57:17 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 26.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: bridge.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bridge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bridge_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/bridge.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bridge/DESCRIPTION’ ... OK * this is package ‘bridge’ version ‘1.56.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘bridge’ 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 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 ‘rama’ which was already attached by Depends. Please remove these calls from your code. Package in Depends field not imported from: ‘rama’ 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 File ‘bridge/R/zzz.R’: .onLoad calls: require("rama", quietly = TRUE) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. bridge.2samples: no visible global function definition for ‘var’ bridge.2samples: no visible global function definition for ‘median’ bridge.2samples: no visible global function definition for ‘mad’ bridge.3samples: no visible global function definition for ‘median’ bridge.3samples: no visible global function definition for ‘mad’ Undefined global functions or variables: mad median var Consider adding importFrom("stats", "mad", "median", "var") to your NAMESPACE file. * 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 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 File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/bridge/libs/bridge.so’: Found ‘_printf’, possibly from ‘printf’ (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. 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’ ... 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/bridge.Rcheck/00check.log’ for details.
bridge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bridge ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘bridge’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bridge2.affy.c -o bridge2.affy.o bridge2.affy.c:37:7: warning: unused variable 'count_model' [-Wunused-variable] int count_model=0; ^ bridge2.affy.c:36:7: warning: unused variable 'old_model' [-Wunused-variable] int old_model; ^ bridge2.affy.c:302:3: warning: implicit declaration of function 'dirichlet' is invalid in C99 [-Wimplicit-function-declaration] dirichlet(gamma, 2, w); ^ bridge2.affy.c:282:10: warning: unused variable 'w_new' [-Wunused-variable] double w_new[2]; ^ 4 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bridge2.c -o bridge2.o bridge2.c:174:7: warning: unused variable 'counta_eps' [-Wunused-variable] int counta_eps=0; ^ bridge2.c:173:7: warning: unused variable 'counta' [-Wunused-variable] int counta=0; ^ bridge2.c:192:10: warning: unused variable 'sum_res2' [-Wunused-variable] double sum_res2; ^ bridge2.c:159:10: warning: unused variable 'post_mean_mu' [-Wunused-variable] double post_mean_mu=0,post_prec_mu=0; ^ bridge2.c:191:10: warning: unused variable 'sum_res1' [-Wunused-variable] double sum_res1; ^ bridge2.c:175:7: warning: unused variable 'countb_eps' [-Wunused-variable] int countb_eps=0; ^ bridge2.c:145:10: warning: unused variable 'pi' [-Wunused-variable] double pi=3.14; ^ bridge2.c:159:25: warning: unused variable 'post_prec_mu' [-Wunused-variable] double post_mean_mu=0,post_prec_mu=0; ^ bridge2.c:177:7: warning: unused variable 'countp' [-Wunused-variable] int countp=0; ^ bridge2.c:160:10: warning: unused variable 'post_mean_beta' [-Wunused-variable] double post_mean_beta=0,post_prec_beta=0; ^ bridge2.c:160:27: warning: unused variable 'post_prec_beta' [-Wunused-variable] double post_mean_beta=0,post_prec_beta=0; ^ bridge2.c:198:18: warning: unused variable 'width_b' [-Wunused-variable] double old_b=0,width_b=5; ^ bridge2.c:166:22: warning: unused variable 'b_eps_new' [-Wunused-variable] double a_eps_new=0,b_eps_new=0; ^ bridge2.c:166:10: warning: unused variable 'a_eps_new' [-Wunused-variable] double a_eps_new=0,b_eps_new=0; ^ bridge2.c:198:10: warning: unused variable 'old_b' [-Wunused-variable] double old_b=0,width_b=5; ^ bridge2.c:171:7: warning: unused variable 'countrho' [-Wunused-variable] int countrho=0; ^ bridge2.c:199:18: warning: unused variable 'width_a' [-Wunused-variable] double old_a=0,width_a=5; ^ bridge2.c:154:10: warning: unused variable 'dens_t' [-Wunused-variable] double dens_t=0,dens_t_new=0; ^ bridge2.c:199:10: warning: unused variable 'old_a' [-Wunused-variable] double old_a=0,width_a=5; ^ bridge2.c:154:19: warning: unused variable 'dens_t_new' [-Wunused-variable] double dens_t=0,dens_t_new=0; ^ bridge2.c:163:26: warning: unused variable 'post_prec_eta' [-Wunused-variable] double post_mean_eta=0,post_prec_eta=0; ^ bridge2.c:138:10: warning: unused variable 'rho_new' [-Wunused-variable] double rho_new; ^ bridge2.c:165:10: warning: unused variable 'l_ab' [-Wunused-variable] double l_ab=0,l_ab_new=0; ^ bridge2.c:165:17: warning: unused variable 'l_ab_new' [-Wunused-variable] double l_ab=0,l_ab_new=0; ^ bridge2.c:161:10: warning: unused variable 'post_mean_alpha' [-Wunused-variable] double post_mean_alpha=0,post_prec_alpha=0; ^ bridge2.c:142:10: warning: unused variable 'sum_rho' [-Wunused-variable] double sum_rho=0,sum_rho_new=0; ^ bridge2.c:161:28: warning: unused variable 'post_prec_alpha' [-Wunused-variable] double post_mean_alpha=0,post_prec_alpha=0; ^ bridge2.c:142:20: warning: unused variable 'sum_rho_new' [-Wunused-variable] double sum_rho=0,sum_rho_new=0; ^ bridge2.c:162:10: warning: unused variable 'post_mean_delta' [-Wunused-variable] double post_mean_delta=0,post_prec_delta=0; ^ bridge2.c:162:28: warning: unused variable 'post_prec_delta' [-Wunused-variable] double post_mean_delta=0,post_prec_delta=0; ^ bridge2.c:143:19: warning: unused variable 'dens_rho_new' [-Wunused-variable] double dens_rho,dens_rho_new; ^ bridge2.c:143:10: warning: unused variable 'dens_rho' [-Wunused-variable] double dens_rho,dens_rho_new; ^ bridge2.c:163:10: warning: unused variable 'post_mean_eta' [-Wunused-variable] double post_mean_eta=0,post_prec_eta=0; ^ 33 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bridge2_util.c -o bridge2_util.o bridge2_util.c:570:5: warning: implicit declaration of function 'dqrdc2_' is invalid in C99 [-Wimplicit-function-declaration] F77_CALL(dqrdc2)(xt, &n, &n, &p, &tol, &rank,qraux, pivot, work); ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:77:1: note: expanded from here dqrdc2_ ^ bridge2_util.c:585:5: warning: implicit declaration of function 'dqrcf_' is invalid in C99 [-Wimplicit-function-declaration] F77_CALL(dqrcf)(xt, &n, &rank, qraux,yt, &n, coeft, &info); ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:78:1: note: expanded from here dqrcf_ ^ bridge2_util.c:549:11: warning: unused variable 'vmax' [-Wunused-variable] char *vmax; ^ bridge2_util.c:608:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ bridge2_util.c:655:11: warning: unused variable 'k' [-Wunused-variable] int i,j,k; ^ bridge2_util.c:693:5: warning: implicit declaration of function 'dqrdc2_' is invalid in C99 [-Wimplicit-function-declaration] F77_CALL(dqrdc2)(xtmp, &n, &n, &p, &tol, &rank,qraux, pivot, work); ^ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:92:22: note: expanded from macro 'F77_CALL' # define F77_CALL(x) x ## _ ^ <scratch space>:79:1: note: expanded from here dqrdc2_ ^ 6 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bridge3.c -o bridge3.o bridge3.c:38:7: warning: unused variable 'count_model' [-Wunused-variable] int count_model=0; ^ bridge3.c:37:7: warning: unused variable 'old_model' [-Wunused-variable] int old_model; ^ bridge3.c:332:25: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses] else if((w_star[3]<u) & u<w_star[4]) ^~~~~~~~~~~~~ bridge3.c:332:25: note: place parentheses around the '<' expression to silence this warning else if((w_star[3]<u) & u<w_star[4]) ^ ( ) bridge3.c:332:25: note: place parentheses around the & expression to evaluate it first else if((w_star[3]<u) & u<w_star[4]) ^ ( ) bridge3.c:362:10: warning: unused variable 'w_new' [-Wunused-variable] double w_new[5]; ^ 4 warnings generated. clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bridge.so bridge2.affy.o bridge2.o bridge2_util.o bridge3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-bridge/00new/bridge/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 (bridge)
bridge.Rcheck/bridge-Ex.timings
name | user | system | elapsed | |
bridge.2samples | 0.194 | 0.007 | 0.202 | |
bridge.3samples | 0.009 | 0.001 | 0.010 | |