Raphael Gottardo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rama |
| Branch: RELEASE_3_9 |
| Last Commit: 3519fd0 |
| Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:55:19 -0400 (Wed, 16 Oct 2019).
| Package 1307/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rama 1.58.0 Raphael Gottardo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rama |
| Version: 1.58.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rama.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rama_1.58.0.tar.gz |
| StartedAt: 2019-10-16 04:16:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:17:12 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 29.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rama.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rama.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rama_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rama.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.58.0’
* 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 ‘rama’ can be installed ... WARNING
Found the following significant warnings:
estimation_slice.c:484:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
estimation_slice.c:493:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:629:17: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
util.c:629:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:636:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:643:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:703:17: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
util.c:703:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:710:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:717:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:767:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:775:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:822:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:830:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:876:17: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
util.c:876:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:883:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:890:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:935:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:944:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:1019:17: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
util.c:1019:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:1026:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:1033:8: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:1100:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:1108:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:1248:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
util.c:1256:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.9-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’
ratio.plot: no visible global function definition for ‘plot’
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 plot quantile
Consider adding
importFrom("grDevices", "grey")
importFrom("graphics", "image", "plot")
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 ‘/home/biocbuild/bbs-3.9-bioc/R/library/rama/libs/rama.so’:
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
weight.plot 5.235 0 5.268
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/rama.Rcheck/00check.log’
for details.
rama.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rama
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘rama’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c estimation_slice.c -o estimation_slice.o
estimation_slice.c: In function ‘mcmc_shift’:
estimation_slice.c:122:10: warning: unused variable ‘SSeps_sd_new’ [-Wunused-variable]
double SSeps_sd_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: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:116:10: warning: unused variable ‘SSR1’ [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^~~~
estimation_slice.c:115:25: warning: unused variable ‘dens_epsilon_new’ [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=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:114:10: warning: unused variable ‘l_epsilon’ [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^~~~~~~~~
estimation_slice.c:113:27: warning: unused variable ‘lambda_eps2_new’ [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^~~~~~~~~~~~~~~
estimation_slice.c:113:10: warning: unused variable ‘lambda_eps1_new’ [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^~~~~~~~~~~~~~~
estimation_slice.c: In function ‘slice_sampling_lambda_eps’:
estimation_slice.c:484:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
while(J>0 & z0 & z0 & (z0 & (zlog_f_L & mLlog_f_R & mR>R)
~^~~~~~~~
util.c:613:13: warning: unused variable ‘v’ [-Wunused-variable]
double u, v, L, R, z, a1;
^
util.c: In function ‘slice_sampling_b’:
util.c:703:17: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
while(K>0 & (z0 & (zlog_f_L & mLlog_f_R & mR>R)
~^~~~~~~~
util.c:686:13: warning: unused variable ‘v’ [-Wunused-variable]
double u, v, L, R, z, b1;
^
util.c: In function ‘slice_sampling_b2’:
util.c:767:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
while(J>0 & z0 & z0 & z0 & z0 & (z0 & (zlog_f_L & mLlog_f_R & mR>R)
~^~~~~~~~
util.c:860:13: warning: unused variable ‘v’ [-Wunused-variable]
double u, v, L, R, z, rho_new;
^
util.c: In function ‘slice_sampling_rho2’:
util.c:935:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
while(J>0 & z0 & z0 & (z0 & (zlog_f_L & mLlog_f_R & mR>R)
~^~~~~~~~
util.c:1000:13: warning: unused variable ‘v’ [-Wunused-variable]
double u, v, L, R, z, shift_new;
^
util.c: In function ‘slice_sampling_shift2’:
util.c:1100:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
while(J>0 & z0 & z0 & z0 & z
rama.Rcheck/rama-Ex.timings
| name | user | system | elapsed | |
| arrange.row | 0.135 | 0.000 | 0.136 | |
| est.shift | 0.363 | 0.000 | 0.364 | |
| fit.model | 0.364 | 0.004 | 0.367 | |
| is.row.na | 0.000 | 0.000 | 0.001 | |
| ls.effect | 0.162 | 0.008 | 0.170 | |
| mat.mean | 0.161 | 0.004 | 0.168 | |
| ratio.plot | 0.424 | 0.000 | 0.424 | |
| weight.plot | 5.235 | 0.000 | 5.268 | |