Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 337/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chopsticks 1.71.0  (landing page)
Hin-Tak Leung
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/chopsticks
git_branch: devel
git_last_commit: 37ef827
git_last_commit_date: 2024-04-30 10:23:29 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for chopsticks on palomino4

To the developers/maintainers of the chopsticks package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chopsticks.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: chopsticks
Version: 1.71.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chopsticks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chopsticks_1.71.0.tar.gz
StartedAt: 2024-06-10 00:53:33 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:55:01 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 88.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chopsticks.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chopsticks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chopsticks_1.71.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/chopsticks.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'chopsticks/DESCRIPTION' ... OK
* this is package 'chopsticks' version '1.71.0'
* 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 'chopsticks' can be installed ... WARNING
Found the following significant warnings:
  inputNew.c:612:17: warning: format '%d' expects a matching 'int' argument [-Wformat=]
  inputNew.c:687:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:408:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:406:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:404:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:401:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:398:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  inputNew.c:395:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  readped.c:233:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 80 [-Wformat-truncation=]
See 'F:/biocbuild/bbs-3.20-bioc/meat/chopsticks.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) for.exercise.Rd:29-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) for.exercise.Rd:34-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) for.exercise.Rd:40-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glm.test.control.Rd:30-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) glm.test.control.Rd:33-37: Lost braces in \enumerate; meant \describe ?
prepare_Rd: ibs.stats.Rd:28: Dropping empty section \references
prepare_Rd: ibs.stats.Rd:49: Dropping empty section \seealso
prepare_Rd: read.pedfile.info.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.pedfile.map.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.snps.chiamo.Rd:37-38: Dropping empty section \note
checkRd: (-1) read.snps.long.old.Rd:81: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) read.snps.long.old.Rd:82: Lost braces in \enumerate; meant \describe ?
prepare_Rd: read.wtccc.signals.Rd:58: Dropping empty section \seealso
checkRd: (-1) read.wtccc.signals.Rd:30: Escaped LaTeX specials: \_ \_
checkRd: (-1) snp.lhs.tests.Rd:36: Lost braces
    36 |     new terms to be tested. See\ code{\link{glm.test.control}}}
       |                                      ^
checkRd: (-1) snp.rhs.tests.Rd:42: Lost braces
    42 |     new terms to be tested. See\ code{\link{glm.test.control}}}
       |                                      ^
checkRd: (-1) snpMatrix-package.Rd:21: Escaped LaTeX specials: \_ \_
checkRd: (-1) testdata.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:26-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:33-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testdata.Rd:39: Lost braces in \itemize; meant \describe ?
prepare_Rd: wtccc.sample.list.Rd:36-37: Dropping empty section \note
prepare_Rd: wtccc.sample.list.Rd:39-40: Dropping empty section \examples
checkRd: (-1) wtccc.sample.list.Rd:26: Escaped LaTeX specials: \_ \_
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'snpMatrix-package.Rd':
  'snpMatrix-package'
* 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* 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 'F:/biocbuild/bbs-3.20-bioc/R/library/chopsticks/libs/x64/chopsticks.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'chopsticks/libs/x64/chopsticks.dll':
  Found non-API call to R: 'R_data_class'

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 nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/chopsticks.Rcheck/00check.log'
for details.


Installation output

chopsticks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL chopsticks
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'chopsticks' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c adler32.c -o adler32.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bind.c -o bind.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c compress.c -o compress.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c crc32.c -o crc32.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c deflate.c -o deflate.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c force_hom.c -o force_hom.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_fit':
glm_test.c:107:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  107 |       double *yw = (double *) calloc(N, sizeof(double));
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from glm_test.c:1:
C:/rtools44/x86_64-w64-mingw32.static.posix/include/stdlib.h:536:17: note: in a call to allocation function 'calloc' declared here
  536 |   void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements);
      |                 ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glm_test_R.c -o glm_test_R.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gzio.c -o gzio.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hash_index.c -o hash_index.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ibs.c -o ibs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c in.c -o in.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c infback.c -o infback.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inffast.c -o inffast.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inflate.c -o inflate.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inftrees.c -o inftrees.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c input.c -o input.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inputNew.c -o inputNew.o
inputNew.c: In function 'insnp_new':
inputNew.c:612:17: warning: format '%d' expects a matching 'int' argument [-Wformat=]
  612 |       Rprintf("%d polymorphisms were not SNPs and have been set to NA ");
      |                ~^
      |                 |
      |                 int
inputNew.c: In function 'simplify_names':
inputNew.c:687:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  687 |     strncpy(back, front, MAX_FLD-1);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c: In function 'insnp_new':
inputNew.c:408:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  408 |           strncpy(gtype2, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:406:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  406 |           strncpy(gtype1, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:404:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  404 |           strncpy(gtype1, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:401:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  401 |           strncpy(cscore, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:398:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  398 |           strncpy(snpid, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
inputNew.c:395:11: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  395 |           strncpy(sampid, field, MAX_FLD-1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c input_unsorted.c -o input_unsorted.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ld_with.c -o ld_with.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mla.c -o mla.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c outdata.c -o outdata.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pairwise_linkage.c -o pairwise_linkage.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_chiamo.c -o read_chiamo.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_hapmap.c -o read_hapmap.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_pedfile.c -o read_pedfile.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_signals.c -o read_signals.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readped.c -o readped.o
readped.c: In function 'readped':
readped.c:233:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 80 [-Wformat-truncation=]
  233 |     snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
      |                                 ^~
readped.c:233:5: note: 'snprintf' output between 3 and 93 bytes into a destination of size 81
  233 |     snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sdfpw.c -o sdfpw.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c single_snp_tests.c -o single_snp_tests.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c snp_summary.c -o snp_summary.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c snpmpy.c -o snpmpy.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c solve_cubic.c -o solve_cubic.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c solve_quadratic.c -o solve_quadratic.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c structure.c -o structure.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c trees.c -o trees.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c uncompr.c -o uncompr.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c zutil.c -o zutil.o
gcc -shared -s -static-libgcc -o chopsticks.dll tmp.def adler32.o bind.o compress.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o trees.o uncompr.o zutil.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-chopsticks/00new/chopsticks/libs/x64
** R
** data
** 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 (chopsticks)

Tests output


Example timings

chopsticks.Rcheck/chopsticks-Ex.timings

nameusersystemelapsed
X.snp-class0.100.050.14
X.snp.matrix-class0.060.000.06
epsout.ld.snp0.100.010.12
for.exercise0.580.070.64
ibs.stats0.050.030.08
ibsCount0.200.010.21
ibsDist0.110.000.11
ld.snp0.110.000.11
ld.with0.080.020.09
pair.result.ld.snp0.090.000.10
plot.snp.dprime0.240.000.23
qq.chisq000
read.HapMap.data000
read.snps.chiamo000
read.wtccc.signals000
row.summary0.080.000.08
single.snp.tests0.080.010.09
snp-class000
snp.cbind0.280.040.32
snp.cor0.200.000.23
snp.dprime-class0.080.000.08
snp.lhs.tests0.090.000.09
snp.matrix-class0.080.010.09
snp.pre0.060.020.08
snp.rhs.tests0.080.000.08
testdata0.080.000.08
xxt0.170.000.17