Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:21 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the rama package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rama.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1588/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Raphael Gottardo
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: rama |
Version: 1.72.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rama.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rama_1.72.0.tar.gz |
StartedAt: 2023-04-10 22:05:28 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:05:58 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 29.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rama.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rama.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rama_1.72.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/rama.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rama/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rama’ version ‘1.72.0’ * 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 ‘rama’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'rama' is deprecated and will be removed from Bioconductor See ‘/Users/biocbuild/bbs-3.16-bioc/meat/rama.Rcheck/00install.out’ for details. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE fit.model: no visible global function definition for ‘median’ fit.model: no visible global function definition for ‘mad’ fit.model: no visible global function definition for ‘quantile’ weight.plot: no visible global function definition for ‘image’ weight.plot: no visible global function definition for ‘grey’ Undefined global functions or variables: grey image mad median quantile Consider adding importFrom("grDevices", "grey") importFrom("graphics", "image") importFrom("stats", "mad", "median", "quantile") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: is.row.na.Rd:40: Dropping empty section \keyword prepare_Rd: ls.effect.Rd:38-39: Dropping empty section \details * 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/4.2/Resources/library/rama/libs/rama.so’: Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/rama.Rcheck/00check.log’ for details.
rama.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rama ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘rama’ ... ** 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 estimation_slice.c -o estimation_slice.o estimation_slice.c:116:24: warning: unused variable 'SS12' [-Wunused-variable] double SSR1=0,SSR2=0,SS12=0; ^ estimation_slice.c:116:17: warning: unused variable 'SSR2' [-Wunused-variable] double SSR1=0,SSR2=0,SS12=0; ^ estimation_slice.c:114:10: warning: unused variable 'l_epsilon' [-Wunused-variable] double l_epsilon=0,l_epsilon_new=0; ^ estimation_slice.c:116:10: warning: unused variable 'SSR1' [-Wunused-variable] double SSR1=0,SSR2=0,SS12=0; ^ estimation_slice.c:113:27: warning: unused variable 'lambda_eps2_new' [-Wunused-variable] double lambda_eps1_new, lambda_eps2_new; ^ estimation_slice.c:134:10: warning: variable 'mean_gamma1' set but not used [-Wunused-but-set-variable] double mean_gamma1=0,mean_gamma2=0; ^ estimation_slice.c:113:10: warning: unused variable 'lambda_eps1_new' [-Wunused-variable] double lambda_eps1_new, lambda_eps2_new; ^ estimation_slice.c:115:25: warning: unused variable 'dens_epsilon_new' [-Wunused-variable] double dens_epsilon=0,dens_epsilon_new=0; ^ estimation_slice.c:134:24: warning: variable 'mean_gamma2' set but not used [-Wunused-but-set-variable] double mean_gamma1=0,mean_gamma2=0; ^ estimation_slice.c:115:10: warning: unused variable 'dens_epsilon' [-Wunused-variable] double dens_epsilon=0,dens_epsilon_new=0; ^ estimation_slice.c:114:22: warning: unused variable 'l_epsilon_new' [-Wunused-variable] double l_epsilon=0,l_epsilon_new=0; ^ estimation_slice.c:121:10: warning: unused variable 'SSeps_sd' [-Wunused-variable] double SSeps_sd=0.; ^ estimation_slice.c:117:10: warning: unused variable 'pi' [-Wunused-variable] double pi=3.14; ^ estimation_slice.c:122:10: warning: unused variable 'SSeps_sd_new' [-Wunused-variable] double SSeps_sd_new=0.; ^ 14 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 ex_estimation_slice.c -o ex_estimation_slice.o ex_estimation_slice.c:137:10: warning: unused variable 'sum_res1' [-Wunused-variable] double sum_res1; ^ ex_estimation_slice.c:112:10: warning: unused variable 'pi' [-Wunused-variable] double pi=3.14; ^ ex_estimation_slice.c:138:10: warning: unused variable 'sum_res2' [-Wunused-variable] double sum_res2; ^ ex_estimation_slice.c:129:24: warning: variable 'mean_gamma2' set but not used [-Wunused-but-set-variable] double mean_gamma1=0,mean_gamma2=0; ^ ex_estimation_slice.c:129:10: warning: variable 'mean_gamma1' set but not used [-Wunused-but-set-variable] double mean_gamma1=0,mean_gamma2=0; ^ ex_estimation_slice.c:119:19: warning: unused variable 'dens_t_new' [-Wunused-variable] double dens_t=0,dens_t_new=0; ^ ex_estimation_slice.c:119:10: warning: unused variable 'dens_t' [-Wunused-variable] double dens_t=0,dens_t_new=0; ^ ex_estimation_slice.c:144:10: warning: unused variable 'old_a' [-Wunused-variable] double old_a=0,width_a=1.; ^ ex_estimation_slice.c:143:10: warning: unused variable 'old_b' [-Wunused-variable] double old_b=0,width_b=5.; ^ 9 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 mean.sd.c -o mean.sd.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c reorder.c -o reorder.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c util.c -o util.o util.c:574:11: warning: unused variable 'k' [-Wunused-variable] int i,j,k; ^ util.c:629:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses] while(K>0 & (z<log_f_L | z<log_f_R)) ~~~~^ util.c:629:13: note: place parentheses around the '>' expression to silence this warning while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:629:13: note: place parentheses around the & expression to evaluate it first while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:613:13: warning: unused variable 'v' [-Wunused-variable] double u, v, L, R, z, a1; ^ util.c:703:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses] while(K>0 & (z<log_f_L | z<log_f_R)) ~~~~^ util.c:703:13: note: place parentheses around the '>' expression to silence this warning while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:703:13: note: place parentheses around the & expression to evaluate it first while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:686:13: warning: unused variable 'v' [-Wunused-variable] double u, v, L, R, z, b1; ^ util.c:876:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses] while(K>0 & (z<log_f_L | z<log_f_R)) ~~~~^ util.c:876:13: note: place parentheses around the '>' expression to silence this warning while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:876:13: note: place parentheses around the & expression to evaluate it first while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:860:13: warning: unused variable 'v' [-Wunused-variable] double u, v, L, R, z, rho_new; ^ util.c:1019:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses] while(K>0 & (z<log_f_L | z<log_f_R)) ~~~~^ util.c:1019:13: note: place parentheses around the '>' expression to silence this warning while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:1019:13: note: place parentheses around the & expression to evaluate it first while(K>0 & (z<log_f_L | z<log_f_R)) ^ ( ) util.c:1000:13: warning: unused variable 'v' [-Wunused-variable] double u, v, L, R, z, shift_new; ^ util.c:1082:13: warning: unused variable 'v' [-Wunused-variable] double u, v, L, R, z, shift_new; ^ 10 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 rama.so estimation_slice.o ex_estimation_slice.o mean.sd.o reorder.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-rama/00new/rama/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 Warning: Package 'rama' is deprecated and will be removed from Bioconductor version 3.17 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: Package 'rama' is deprecated and will be removed from Bioconductor version 3.17 ** testing if installed package keeps a record of temporary installation path * DONE (rama)
rama.Rcheck/rama-Ex.timings
name | user | system | elapsed | |
arrange.row | 0.079 | 0.006 | 0.085 | |
est.shift | 0.193 | 0.004 | 0.197 | |
fit.model | 0.295 | 0.003 | 0.299 | |
is.row.na | 0 | 0 | 0 | |
ls.effect | 0.094 | 0.011 | 0.105 | |
mat.mean | 0.067 | 0.003 | 0.070 | |
ratio.plot | 0.188 | 0.003 | 0.191 | |
weight.plot | 2.867 | 0.011 | 2.889 | |