Back to Multiple platform build/check report for BioC 3.15
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-10 13:21:36 -0400 (Mon, 10 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4379
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4133
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4198
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 iPath on palomino3


To the developers/maintainers of the iPath package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iPath.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 976/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iPath 1.2.0  (landing page)
Kenong Su
Snapshot Date: 2022-10-09 13:55:13 -0400 (Sun, 09 Oct 2022)
git_url: https://git.bioconductor.org/packages/iPath
git_branch: RELEASE_3_15
git_last_commit: 5770c5d
git_last_commit_date: 2022-04-26 12:17:18 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: iPath
Version: 1.2.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iPath.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings iPath_1.2.0.tar.gz
StartedAt: 2022-10-10 01:02:56 -0400 (Mon, 10 Oct 2022)
EndedAt: 2022-10-10 01:05:40 -0400 (Mon, 10 Oct 2022)
EllapsedTime: 163.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: iPath.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iPath.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings iPath_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/iPath.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'iPath/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPath' 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 'iPath' 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
water_fall: no visible binding for global variable 'value'
water_fall: no visible binding for global variable 'type'
Undefined global functions or variables:
  type value
* 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 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/iPath/libs/x64/iPath.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (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 ... ERROR
Running examples in 'iPath-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iES_surv
> ### Title: iES calculation Function
> ### Aliases: iES_surv
> ### Keywords: analysis and for groups iPath normal-like. of patients:
> ###   perturbed survival two
> 
> ### ** Examples
> 
> data(PRAD_data)
> data(GSDB_example)
> iES_mat = iES_cal2(prad_exprs, GSDB = GSDB_example)
start normalization ...
start calculating iES matrix ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  51%
  |                                                                            
  |=====================================================                 |  76%
  |                                                                            
  |======================================================================| 100%

> iES_surv(iES_mat, cli = prad_cli, indVec = prad_inds)
Error in if (tmp_mean < mean(tumor_vec)) { : 
  missing value where TRUE/FALSE needed
Calls: iES_surv -> vapply -> FUN
Execution halted
* 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 ERROR, 2 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/iPath.Rcheck/00check.log'
for details.


Installation output

iPath.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL iPath
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'iPath' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CppFunctions.cpp -o CppFunctions.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -shared -s -static-libgcc -o iPath.dll tmp.def CppFunctions.o RcppExports.o -fopenmp -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-iPath/00new/iPath/libs/x64
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iPath)

Tests output


Example timings

iPath.Rcheck/iPath-Ex.timings

nameusersystemelapsed
GSDB_example0.010.000.02
density_fall 2.82 0.2521.18
iES_cal2 1.62 0.2321.10