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 12:19:12 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rama.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rama_1.58.0.tar.gz |
| StartedAt: 2019-10-16 06:19:54 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:20:40 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 45.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rama.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rama.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rama_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rama.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 'C:/Users/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/rama/libs/i386/rama.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/rama/libs/x64/rama.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
weight.plot 6.6 0 6.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
weight.plot 5.15 0.02 5.17
* 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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/rama.Rcheck/00check.log'
for details.
rama.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rama_1.58.0.tar.gz && rm -rf rama.buildbin-libdir && mkdir rama.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rama.buildbin-libdir rama_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rama_1.58.0.zip && rm rama_1.58.0.tar.gz rama_1.58.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 324k 100 324k 0 0 2098k 0 --:--:-- --:--:-- --:--:-- 2194k
install for i386
* installing *source* package 'rama' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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 & z0 & 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
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rama.Rcheck/examples_i386/rama-Ex.timings
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rama.Rcheck/examples_x64/rama-Ex.timings
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