Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:07:43 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 HEM on riesling1


To the developers/maintainers of the HEM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HEM.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 863/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HEM 1.67.0  (landing page)
HyungJun Cho
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/HEM
git_branch: master
git_last_commit: de59b48
git_last_commit_date: 2021-10-26 11:47:04 -0400 (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: HEM
Version: 1.67.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HEM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HEM_1.67.0.tar.gz
StartedAt: 2022-03-17 19:18:09 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:19:03 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 53.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HEM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HEM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HEM_1.67.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/HEM.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HEM/DESCRIPTION' ... OK
* this is package 'HEM' version '1.67.0'
* 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 whether package 'HEM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/HEM/libs/x64/HEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'putchar', possibly from 'putchar' (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 ... 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
  'D:/biocbuild/bbs-3.15-bioc/meat/HEM.Rcheck/00check.log'
for details.



Installation output

HEM.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'HEM' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c hem.c -o hem.o
hem.c: In function 'onelayerhem':
hem.c:1390:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
  int i, j, k, m, n;
            ^
hem.c: In function 'chk_prt':
hem.c:1593:16: warning: variable 'l' set but not used [-Wunused-but-set-variable]
   int i, j, k, l;
                ^
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o HEM.dll tmp.def hem.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-HEM/00new/HEM/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HEM'
    finding HTML links ... done
    am.tran                                 html  
    am.tran.half                            html  
    base.ASE.Olig                           html  
    base.PSE.Olig                           html  
    base.error.Olig                         html  
    base.error.Olig.quanOnly                html  
    boot.base.ASE.Olig                      html  
    boot.base.PSE.Olig                      html  
    boot.base.error.Olig                    html  
    fixbound.predict.smooth.spline          html  
    hem                                     html  
    hem.eb.prior                            html  
    hem.fdr                                 html  
    hem.null.no                             html  
    hem.null.one                            html  
    hem.null.two                            html  
    hem.preproc                             html  
    mubcp                                   html  
    nonpar.error.Olig                       html  
    nonpar.no.error.Olig                    html  
    nonpar.rep.error.Olig                   html  
    par.error.Olig                          html  
    par.no.error.Olig                       html  
    par.rep.error.Olig                      html  
    pbrain                                  html  
    permut                                  html  
    quant.norm                              html  
    quant.normal                            html  
    quant.normal2                           html  
    quant.normalize                         html  
    remove.sig.genes                        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
* DONE (HEM)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RTCA' is missing or broken
 done

Tests output


Example timings

HEM.Rcheck/HEM-Ex.timings

nameusersystemelapsed
hem0.080.000.13
hem.eb.prior0.060.000.09
hem.fdr0.010.000.03
hem.preproc0.020.000.01