David Clayton
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/snpStats |
| git_branch: RELEASE_3_16 |
| git_last_commit: 7d4cec7 |
| git_last_commit_date: 2022-11-01 11:03:45 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:53 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the snpStats package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snpStats.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. |
| Package 1912/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| snpStats 1.48.0 (landing page) David Clayton
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: snpStats |
| Version: 1.48.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:snpStats.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings snpStats_1.48.0.tar.gz |
| StartedAt: 2023-04-11 06:13:13 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 06:14:41 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 87.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: snpStats.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:snpStats.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings snpStats_1.48.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/snpStats.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'snpStats/DESCRIPTION' ... OK
* this is package 'snpStats' version '1.48.0'
* 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 'snpStats' can be installed ... WARNING
Found the following significant warnings:
input.c:788:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:442:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:438:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:435:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:432:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:429:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
readped.c:234:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 127 [-Wformat-truncation=]
testBig.c:31:27: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See 'F:/biocbuild/bbs-3.16-bioc/meat/snpStats.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 4.1Mb
* 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 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-3.16-bioc/R/library/snpStats/libs/x64/snpStats.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
File 'snpStats/libs/x64/snpStats.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. 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 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 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/snpStats.Rcheck/00check.log'
for details.
snpStats.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL snpStats
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'snpStats' ...
** using staged installation
** libs
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Runcertain.c -o Runcertain.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bind.c -o bind.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c count_gt.c -o count_gt.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c covwin.c -o covwin.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c force_hom.c -o force_hom.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fst.c -o fst.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c glm_test.c -o glm_test.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:368:7: warning: unused variable 'max_name_length' [-Wunused-variable]
368 | int max_name_length = MAX_NAME_LENGTH -1;
| ^~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hash_index.c -o hash_index.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hphase.c -o hphase.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c imputation.c -o imputation.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c in.c -o in.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input.c -o input.o
input.c: In function 'simplify_names':
input.c:788:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
788 | strncpy(back, front, MAX_FLD-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c: In function 'insnp_new':
input.c:442:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
442 | strncpy(gtype2, field, MAX_FLD-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:438:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
438 | strncpy(gtype1, field, MAX_FLD-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:435:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
435 | strncpy(cscore, field, MAX_FLD-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:432:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
432 | strncpy(snpid, field, MAX_FLD-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:429:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
429 | strncpy(sampid, field, MAX_FLD-1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c invert.c -o invert.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ipf.c -o ipf.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ld.c -o ld.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c misc.c -o misc.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mla.c -o mla.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mvphenotype.c -o mvphenotype.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c outdata.c -o outdata.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c plink.c -o plink.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_uncertain.c -o read_uncertain.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readped.c -o readped.o
readped.c: In function 'readped':
readped.c:234:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 127 [-Wformat-truncation=]
234 | snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
| ^~
readped.c:234:5: note: 'snprintf' output between 3 and 140 bytes into a destination of size 128
234 | snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c single_snp_tests.c -o single_snp_tests.o
single_snp_tests.c: In function 'score_single':
single_snp_tests.c:223:4: warning: 'name_index' may be used uninitialized in this function [-Wmaybe-uninitialized]
223 | do_impute(Snps, n, NULL, subset, nsubj, name_index, Rule, gt2ht,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | xadd, xdom);
| ~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c snp_summary.c -o snp_summary.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c snpmpy.c -o snpmpy.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c solve_cubic.c -o solve_cubic.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c structure.c -o structure.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c subset.c -o subset.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c switch.c -o switch.o
switch.c: In function 'test_switch':
switch.c:32:8: warning: variable 'female2' set but not used [-Wunused-but-set-variable]
32 | int *female2 = NULL;
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tdt.c -o tdt.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c testBig.c -o testBig.o
testBig.c: In function 'snp_big':
testBig.c:31:27: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
31 | sprintf(name, "Subject%d", i+1);
| ^~
testBig.c:31:19: note: directive argument in the range [1, 2147483647]
31 | sprintf(name, "Subject%d", i+1);
| ^~~~~~~~~~~
testBig.c:31:5: note: 'sprintf' output between 9 and 18 bytes into a destination of size 16
31 | sprintf(name, "Subject%d", i+1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c uncertain.c -o uncertain.o
gcc -shared -s -static-libgcc -o snpStats.dll tmp.def Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o subset.o switch.o tdt.o testBig.o uncertain.o -LF:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-snpStats/00new/snpStats/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 (snpStats)
snpStats.Rcheck/snpStats-Ex.timings
| name | user | system | elapsed | |
| Fst | 0.47 | 0.03 | 0.50 | |
| GlmEstimates-class | 0 | 0 | 0 | |
| GlmTests-class | 0 | 0 | 0 | |
| ImputationRules-class | 0 | 0 | 0 | |
| SingleSnpTests-class | 0 | 0 | 0 | |
| SnpMatrix-class | 0.13 | 0.01 | 0.14 | |
| XSnpMatrix-class | 0.07 | 0.00 | 0.08 | |
| chi.squared | 0.07 | 0.00 | 0.06 | |
| families | 0.01 | 0.00 | 0.02 | |
| filter.rules | 0 | 0 | 0 | |
| for.exercise | 0.94 | 0.00 | 0.93 | |
| ibsCount | 0.33 | 0.00 | 0.33 | |
| ibsDist | 0.26 | 0.00 | 0.27 | |
| imputation.maf | 0 | 0 | 0 | |
| impute.snps | 0.58 | 0.02 | 0.60 | |
| ld | 0.06 | 0.00 | 0.06 | |
| mean2g | 0.06 | 0.00 | 0.06 | |
| misinherits | 0.05 | 0.01 | 0.06 | |
| mvtests | 0 | 0 | 0 | |
| plotUncertainty | 0 | 0 | 0 | |
| pool | 0.16 | 0.00 | 0.16 | |
| pp | 0.14 | 0.00 | 0.14 | |
| qq.chisq | 0 | 0 | 0 | |
| random.snps | 0.01 | 0.00 | 0.02 | |
| read.beagle | 0 | 0 | 0 | |
| read.impute | 0 | 0 | 0 | |
| read.long | 0 | 0 | 0 | |
| read.mach | 0 | 0 | 0 | |
| read.pedfile | 0 | 0 | 0 | |
| row.summary | 0.11 | 0.00 | 0.11 | |
| single.snp.tests | 0.08 | 0.02 | 0.09 | |
| sm.compare | 0 | 0 | 0 | |
| snp.cor | 0.31 | 0.00 | 0.31 | |
| snp.imputation | 0.55 | 0.00 | 0.54 | |
| snp.lhs.estimates | 0.25 | 0.03 | 0.29 | |
| snp.lhs.tests | 0.08 | 0.02 | 0.09 | |
| snp.pre.multiply | 0.08 | 0.03 | 0.11 | |
| snp.rhs.estimates | 0.12 | 0.02 | 0.14 | |
| snp.rhs.tests | 0.09 | 0.00 | 0.09 | |
| switch.alleles | 0.05 | 0.03 | 0.08 | |
| tdt.snp | 0.02 | 0.01 | 0.03 | |
| test.allele.switch | 0.07 | 0.02 | 0.10 | |
| testdata | 0.11 | 0.00 | 0.11 | |
| write.plink | 0.14 | 0.03 | 0.17 | |
| xxt | 0.19 | 0.02 | 0.20 | |