Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:06:46 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 tokay2


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? 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 951/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iPath 1.0.0  (landing page)
Kenong Su
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/iPath
git_branch: RELEASE_3_14
git_last_commit: 10fca6d
git_last_commit_date: 2021-10-26 13:11:25 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: iPath
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iPath.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iPath_1.0.0.tar.gz
StartedAt: 2022-01-25 21:41:47 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 21:46:04 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 256.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: iPath.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iPath.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iPath_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/iPath.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iPath/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPath' version '1.0.0'
* 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
* 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
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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/iPath/libs/i386/iPath.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/iPath/libs/x64/iPath.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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' ... ERROR
Running examples in 'iPath-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: density_fall
> ### Title: density fall plot
> ### Aliases: density_fall
> ### Keywords: and densityfall for normal plot sample. tumor
> 
> ### ** Examples
> 
> data(PRAD_data)
> data(GSDB_example)
> iES_mat = iES_cal2(prad_exprs, GSDB = GSDB_example)
start normalization ...
start calculating iES matrix ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%Error in env[[as.character(i)]] <- value : 
  wrong args for environment subassignment
Calls: iES_cal2 ... bploop -> bploop.iterate -> <Anonymous> -> add_inorder

Error in serialize(data, node$con) : error writing to connection
Calls: iES_cal2 ... .send_to -> <Anonymous> -> sendData.SOCKnode -> serialize
Execution halted
Error in serialize(data, node$con) : error writing to connection
Calls: <Anonymous> ... .send_to -> <Anonymous> -> sendData.SOCKnode -> serialize
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
density_fall 3.55   0.62   19.70
iES_survPlot 3.33   0.59   20.33
water_fall   2.46   0.56   19.99
iES_surv     2.33   0.66   19.89
iES_cal2     2.08   0.61   19.87
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/iPath.Rcheck/00check.log'
for details.


Installation output

iPath.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iPath_1.0.0.tar.gz && rm -rf iPath.buildbin-libdir && mkdir iPath.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iPath.buildbin-libdir iPath_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iPath_1.0.0.zip && rm iPath_1.0.0.tar.gz iPath_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 31 2603k   31  825k    0     0  1321k      0  0:00:01 --:--:--  0:00:01 1320k
100 2603k  100 2603k    0     0  1753k      0  0:00:01  0:00:01 --:--:-- 1754k

install for i386

* installing *source* package 'iPath' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CppFunctions.cpp -o CppFunctions.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o iPath.dll tmp.def CppFunctions.o RcppExports.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/iPath.buildbin-libdir/00LOCK-iPath/00new/iPath/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iPath'
    finding HTML links ... done
    GSDB_example                            html  
    GSEA                                    html  
    density_fall                            html  
    iES_cal2                                html  
    iES_surv                                html  
    iES_survPlot                            html  
    prad_cli                                html  
    prad_exprs                              html  
    prad_inds                               html  
    rem_data                                html  
    setUp_BPPARAM                           html  
    water_fall                              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 'iPath' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CppFunctions.cpp -o CppFunctions.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o iPath.dll tmp.def CppFunctions.o RcppExports.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/iPath.buildbin-libdir/iPath/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iPath' as iPath_1.0.0.zip
* DONE (iPath)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'iPath' successfully unpacked and MD5 sums checked

Tests output


Example timings

iPath.Rcheck/examples_i386/iPath-Ex.timings

nameusersystemelapsed
GSDB_example000

iPath.Rcheck/examples_x64/iPath-Ex.timings

nameusersystemelapsed
GSDB_example000
density_fall 3.55 0.6219.70
iES_cal2 2.08 0.6119.87
iES_surv 2.33 0.6619.89
iES_survPlot 3.33 0.5920.33
prad_cli0.260.020.28
prad_exprs0.30.00.3
prad_inds0.270.030.29
water_fall 2.46 0.5619.99