Farhad Shokoohi
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/fmrs |
| git_branch: RELEASE_3_13 |
| git_last_commit: 0aa7bb6 |
| git_last_commit_date: 2021-05-19 12:53:33 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the fmrs package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fmrs.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 671/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fmrs 1.2.0 (landing page) Farhad Shokoohi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: fmrs |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fmrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fmrs_1.2.0.tar.gz |
| StartedAt: 2021-10-14 23:18:23 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:19:39 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 75.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fmrs.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fmrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings fmrs_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fmrs.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'fmrs/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'fmrs' version '1.2.0' * package encoding: UTF-8 * 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 'fmrs' 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 * 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 ... OK * 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 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-3.13-bioc/R/library/fmrs/libs/i386/fmrs.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/fmrs/libs/x64/fmrs.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) 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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' 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 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/fmrs.Rcheck/00check.log' for details.
fmrs.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/fmrs_1.2.0.tar.gz && rm -rf fmrs.buildbin-libdir && mkdir fmrs.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fmrs.buildbin-libdir fmrs_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL fmrs_1.2.0.zip && rm fmrs_1.2.0.tar.gz fmrs_1.2.0.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 37572 100 37572 0 0 316k 0 --:--:-- --:--:-- --:--:-- 319k
install for i386
* installing *source* package 'fmrs' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fmrs.c -o fmrs.o
fmrs.c: In function 'minimum':
fmrs.c:138:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i = 0; i < ncov1; i++)
^~~
fmrs.c:142:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
return(min1);
^~~~~~
fmrs.c: In function 'maximum':
fmrs.c:152:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i = 0; i < ncov1; i++)
^~~
fmrs.c:156:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
return(max1);
^~~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_MLE':
fmrs.c:457:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:463:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:285:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_VarSel':
fmrs.c:883:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < NCOV; j++)
^~~
fmrs.c:887:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for(i = 0; i < ONCOV[k1]; i++){
^~~
fmrs.c:915:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:921:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:687:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Norm_Surv_CwTuneParSel':
fmrs.c:1403:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:1409:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:1218:12: warning: variable 'new_pi0' set but not used [-Wunused-but-set-variable]
double new_pi0[NCOMP];
^~~~~~~
fmrs.c:1211:12: warning: variable 'new_sigma0' set but not used [-Wunused-but-set-variable]
double new_sigma0[NCOMP];
^~~~~~~~~~
fmrs.c:1196:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_MLE':
fmrs.c:1752:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:1758:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:1547:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_VarSel':
fmrs.c:2205:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (NCOV + 1); j++)
^~~
fmrs.c:2212:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for(i = 0; i < (NCOV + 1); i++){
^~~
fmrs.c:2251:15: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (NCOV + 2); j++)
^~~
fmrs.c:2257:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (NCOV + 2); i++) {
^~~
fmrs.c:2271:19: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (NCOV + 1); j++)
^~~
fmrs.c:2277:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
sumi5[k1] = 0.0;
^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_CwTuneParSel':
fmrs.c:2745:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < NCOV; j++)
^~~
fmrs.c:2750:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for(i = 0; i < ONCOV[k1]; i++){
^~~
fmrs.c:2553:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][k1];
^~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_VarSel':
fmrs.c:748:12: warning: 'sat_den' may be used uninitialized in this function [-Wmaybe-uninitialized]
double sat_den;
^~~~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_VarSel':
fmrs.c:2072:12: warning: 'sat_den' may be used uninitialized in this function [-Wmaybe-uninitialized]
double sat_den;
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fmrs_init.c -o fmrs_init.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o fmrs.dll tmp.def fmrs.o fmrs_init.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/fmrs.buildbin-libdir/00LOCK-fmrs/00new/fmrs/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'fmrs'
finding HTML links ... done
BIC-methods html
coefficients-methods html
dispersion-methods html
fitted-methods html
fmrs-package html
fmrs.gendata-methods html
fmrs.mle-methods html
fmrs.tunsel-methods html
fmrs.varsel-methods html
fmrsfit-class html
fmrstunpar-class html
logLik-methods html
mixProp-methods html
ncomp-methods html
ncov-methods html
nobs-methods html
residuals-methods html
summary-methods html
weights-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'fmrs' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fmrs.c -o fmrs.o
fmrs.c: In function 'minimum':
fmrs.c:138:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i = 0; i < ncov1; i++)
^~~
fmrs.c:142:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
return(min1);
^~~~~~
fmrs.c: In function 'maximum':
fmrs.c:152:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(i = 0; i < ncov1; i++)
^~~
fmrs.c:156:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
return(max1);
^~~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_MLE':
fmrs.c:457:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:463:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:285:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_VarSel':
fmrs.c:883:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < NCOV; j++)
^~~
fmrs.c:887:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for(i = 0; i < ONCOV[k1]; i++){
^~~
fmrs.c:915:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:921:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:687:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Norm_Surv_CwTuneParSel':
fmrs.c:1403:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:1409:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:1218:12: warning: variable 'new_pi0' set but not used [-Wunused-but-set-variable]
double new_pi0[NCOMP];
^~~~~~~
fmrs.c:1211:12: warning: variable 'new_sigma0' set but not used [-Wunused-but-set-variable]
double new_sigma0[NCOMP];
^~~~~~~~~~
fmrs.c:1196:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_MLE':
fmrs.c:1752:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (ONCOV[k1] + 1); j++)
^~~
fmrs.c:1758:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (ONCOV[k1] + 1); i++) {
^~~
fmrs.c:1547:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][NCOMP];
^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_VarSel':
fmrs.c:2205:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (NCOV + 1); j++)
^~~
fmrs.c:2212:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for(i = 0; i < (NCOV + 1); i++){
^~~
fmrs.c:2251:15: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (NCOV + 2); j++)
^~~
fmrs.c:2257:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (i = 0; i < (NCOV + 2); i++) {
^~~
fmrs.c:2271:19: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < (NCOV + 1); j++)
^~~
fmrs.c:2277:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
sumi5[k1] = 0.0;
^~~~~
fmrs.c: In function 'FMR_Weibl_Surv_CwTuneParSel':
fmrs.c:2745:11: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for(j = 0; j < NCOV; j++)
^~~
fmrs.c:2750:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for(i = 0; i < ONCOV[k1]; i++){
^~~
fmrs.c:2553:12: warning: variable 'multX' set but not used [-Wunused-but-set-variable]
double multX[nsize][NCOV][k1];
^~~~~
fmrs.c: In function 'FMR_Norm_Surv_EM_VarSel':
fmrs.c:748:12: warning: 'sat_den' may be used uninitialized in this function [-Wmaybe-uninitialized]
double sat_den;
^~~~~~~
fmrs.c: In function 'FMR_Weibl_Surv_EM_VarSel':
fmrs.c:2072:12: warning: 'sat_den' may be used uninitialized in this function [-Wmaybe-uninitialized]
double sat_den;
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fmrs_init.c -o fmrs_init.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o fmrs.dll tmp.def fmrs.o fmrs_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/fmrs.buildbin-libdir/fmrs/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fmrs' as fmrs_1.2.0.zip
* DONE (fmrs)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'fmrs' successfully unpacked and MD5 sums checked
|
fmrs.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(fmrs)
BugReports: https://github.com/shokoohi/fmrs/issues
>
> test_check("fmrs")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
2.28 0.18 2.45
|
fmrs.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(fmrs)
BugReports: https://github.com/shokoohi/fmrs/issues
>
> test_check("fmrs")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
1.93 0.12 2.04
|
|
fmrs.Rcheck/examples_i386/fmrs-Ex.timings
|
fmrs.Rcheck/examples_x64/fmrs-Ex.timings
|