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This page was generated on 2022-01-19 11:06:06 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

CHECK results for fmrs on nebbiolo1


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.

raw results

Package 677/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fmrs 1.5.0  (landing page)
Farhad Shokoohi
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/fmrs
git_branch: master
git_last_commit: 3054486
git_last_commit_date: 2021-10-26 13:00:45 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: fmrs
Version: 1.5.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:fmrs.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings fmrs_1.5.0.tar.gz
StartedAt: 2022-01-18 19:15:42 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 19:16:20 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 38.3 seconds
RetCode: 0
Status:   OK  
CheckDir: fmrs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:fmrs.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings fmrs_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/fmrs.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fmrs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fmrs’ version ‘1.5.0’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/fmrs.Rcheck/00check.log’
for details.



Installation output

fmrs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL fmrs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘fmrs’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fmrs.c -o fmrs.o
fmrs.c: In function ‘minimum’:
fmrs.c:138:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  138 |   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’
  142 |     return(min1);
      |     ^~~~~~
fmrs.c: In function ‘maximum’:
fmrs.c:152:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  152 |   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’
  156 |     return(max1);
      |     ^~~~~~
fmrs.c: In function ‘FMR_Norm_Surv_EM_MLE’:
fmrs.c:457:11: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  457 |           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’
  463 |             for (i = 0; i < (ONCOV[k1] + 1); i++) {
      |             ^~~
fmrs.c:285:12: warning: variable ‘multX’ set but not used [-Wunused-but-set-variable]
  285 |     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]
  883 |         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’
  887 |           for(i = 0; i < ONCOV[k1]; i++){
      |           ^~~
fmrs.c:915:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  915 |             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’
  921 |               for (i = 0; i < (ONCOV[k1] + 1); i++) {
      |               ^~~
fmrs.c:687:12: warning: variable ‘multX’ set but not used [-Wunused-but-set-variable]
  687 |     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]
 1403 |           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’
 1409 |             for (i = 0; i < (ONCOV[k1] + 1); i++) {
      |             ^~~
fmrs.c:1218:12: warning: variable ‘new_pi0’ set but not used [-Wunused-but-set-variable]
 1218 |     double new_pi0[NCOMP];
      |            ^~~~~~~
fmrs.c:1211:12: warning: variable ‘new_sigma0’ set but not used [-Wunused-but-set-variable]
 1211 |     double new_sigma0[NCOMP];
      |            ^~~~~~~~~~
fmrs.c:1196:12: warning: variable ‘multX’ set but not used [-Wunused-but-set-variable]
 1196 |     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]
 1752 |             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’
 1758 |               for (i = 0; i < (ONCOV[k1] + 1); i++) {
      |               ^~~
fmrs.c:1547:12: warning: variable ‘multX’ set but not used [-Wunused-but-set-variable]
 1547 |     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]
 2205 |           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’
 2212 |             for(i = 0; i < (NCOV + 1); i++){
      |             ^~~
fmrs.c:2251:15: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2251 |               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’
 2257 |                 for (i = 0; i < (NCOV + 2); i++) {
      |                 ^~~
fmrs.c:2271:19: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2271 |                   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’
 2277 |                     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]
 2745 |           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’
 2750 |             for(i = 0; i < ONCOV[k1]; i++){
      |             ^~~
fmrs.c:2553:12: warning: variable ‘multX’ set but not used [-Wunused-but-set-variable]
 2553 |     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]
  748 |     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]
 2072 |     double sat_den;
      |            ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fmrs_init.c -o fmrs_init.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o fmrs.so fmrs.o fmrs_init.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-fmrs/00new/fmrs/libs
** R
** inst
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fmrs)

Tests output

fmrs.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.520   0.091   1.595 

Example timings

fmrs.Rcheck/fmrs-Ex.timings

nameusersystemelapsed
BIC-methods0.0340.0080.042
coefficients-methods0.3580.0200.378
dispersion-methods0.0340.0000.034
fitted-methods0.0350.0000.035
fmrs.gendata-methods0.0040.0000.004
fmrs.mle-methods0.0370.0010.038
fmrs.tunsel-methods0.0750.0020.077
fmrs.varsel-methods0.1530.0000.154
logLik-methods0.0320.0030.035
mixProp-methods0.0390.0000.039
ncomp-methods0.0340.0000.035
ncov-methods0.0310.0040.035
nobs-methods0.0340.0000.034
residuals-methods0.0350.0000.035
summary-methods0.0790.0000.079
weights-methods0.0350.0000.035