rama 1.48.0
Raphael Gottardo
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/rama | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rama_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rama.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.48.0’
* 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 ... 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 ... 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
File ‘rama/libs/rama.so’:
Found ‘_printf’, possibly from ‘printf’ (C)
Objects: ‘estimation_slice.o’, ‘ex_estimation_slice.o’
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘estimation_slice.o’, ‘ex_estimation_slice.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/rama.Rcheck/00check.log’
for details.
* installing *source* package ‘rama’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c estimation_slice.c -o estimation_slice.o
estimation_slice.c:122:10: warning: unused variable 'SSeps_sd_new' [-Wunused-variable]
double SSeps_sd_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:113:10: warning: unused variable 'lambda_eps1_new' [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^
estimation_slice.c:113:27: warning: unused variable 'lambda_eps2_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:114:22: warning: unused variable 'l_epsilon_new' [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^
estimation_slice.c:117:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
estimation_slice.c:115:10: warning: unused variable 'dens_epsilon' [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=0;
^
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:121:10: warning: unused variable 'SSeps_sd' [-Wunused-variable]
double SSeps_sd=0.;
^
estimation_slice.c:116:10: warning: unused variable 'SSR1' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ex_estimation_slice.c -o ex_estimation_slice.o
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:119:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
ex_estimation_slice.c:112:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
ex_estimation_slice.c:137:10: warning: unused variable 'sum_res1' [-Wunused-variable]
double sum_res1;
^
ex_estimation_slice.c:143:10: warning: unused variable 'old_b' [-Wunused-variable]
double old_b=0,width_b=5.;
^
ex_estimation_slice.c:144:10: warning: unused variable 'old_a' [-Wunused-variable]
double old_a=0,width_a=1.;
^
ex_estimation_slice.c:138:10: warning: unused variable 'sum_res2' [-Wunused-variable]
double sum_res2;
^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mean.sd.c -o mean.sd.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c reorder.c -o reorder.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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 -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 /Users/biocbuild/bbs-3.4-bioc/meat/rama.Rcheck/rama/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rama)