Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 337/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chopsticks 1.73.0 (landing page) Hin-Tak Leung
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: chopsticks |
Version: 1.73.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:chopsticks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings chopsticks_1.73.0.tar.gz |
StartedAt: 2024-12-24 05:19:21 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 05:20:23 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 62.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: chopsticks.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:chopsticks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings chopsticks_1.73.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘chopsticks/DESCRIPTION’ ... OK * this is package ‘chopsticks’ version ‘1.73.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘chopsticks’ can be installed ... WARNING Found the following significant warnings: glm_test.c:107:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * checking installed package size ... INFO installed size is 5.6Mb 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 loading without being on the library search path ... 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 ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/chopsticks/libs/chopsticks.so’: Found ‘sprintf’, possibly from ‘sprintf’ (C) File ‘chopsticks/libs/chopsticks.so’: Found non-API calls to R: ‘R_data_class’, ‘SET_S4_OBJECT’ 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, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. * 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: 3 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/chopsticks.Rcheck/00check.log’ for details.
chopsticks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL chopsticks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘chopsticks’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c adler32.c -o adler32.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bind.c -o bind.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c compress.c -o compress.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c crc32.c -o crc32.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c deflate.c -o deflate.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c force_hom.c -o force_hom.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c glm_test_R.c -o glm_test_R.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c gzio.c -o gzio.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c hash_index.c -o hash_index.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ibs.c -o ibs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c in.c -o in.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c infback.c -o infback.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c inffast.c -o inffast.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c inflate.c -o inflate.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c inftrees.c -o inftrees.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c input.c -o input.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c inputNew.c -o inputNew.o 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c input_unsorted.c -o input_unsorted.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ld_graphic_eps.c -o ld_graphic_eps.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ld_with.c -o ld_with.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c mla.c -o mla.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c outdata.c -o outdata.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pairwise_linkage.c -o pairwise_linkage.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c read_chiamo.c -o read_chiamo.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c read_hapmap.c -o read_hapmap.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c read_pedfile.c -o read_pedfile.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c read_signals.c -o read_signals.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c sdfpw.c -o sdfpw.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c single_snp_tests.c -o single_snp_tests.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c snp_summary.c -o snp_summary.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c snpmpy.c -o snpmpy.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c solve_cubic.c -o solve_cubic.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c solve_quadratic.c -o solve_quadratic.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c structure.c -o structure.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c trees.c -o trees.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c uncompr.c -o uncompr.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c zutil.c -o zutil.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o chopsticks.so 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 -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-chopsticks/00new/chopsticks/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chopsticks)
chopsticks.Rcheck/chopsticks-Ex.timings
name | user | system | elapsed | |
X.snp-class | 0.095 | 0.006 | 0.100 | |
X.snp.matrix-class | 0.082 | 0.000 | 0.083 | |
epsout.ld.snp | 0.113 | 0.004 | 0.117 | |
for.exercise | 0.605 | 0.012 | 0.617 | |
ibs.stats | 0.084 | 0.000 | 0.083 | |
ibsCount | 0.203 | 0.000 | 0.203 | |
ibsDist | 0.114 | 0.000 | 0.114 | |
ld.snp | 0.107 | 0.000 | 0.107 | |
ld.with | 0.084 | 0.000 | 0.085 | |
pair.result.ld.snp | 0.072 | 0.000 | 0.072 | |
plot.snp.dprime | 0.196 | 0.000 | 0.201 | |
qq.chisq | 0 | 0 | 0 | |
read.HapMap.data | 0 | 0 | 0 | |
read.snps.chiamo | 0 | 0 | 0 | |
read.wtccc.signals | 0 | 0 | 0 | |
row.summary | 0.087 | 0.000 | 0.087 | |
single.snp.tests | 0.094 | 0.004 | 0.097 | |
snp-class | 0 | 0 | 0 | |
snp.cbind | 0.396 | 0.000 | 0.397 | |
snp.cor | 0.503 | 0.004 | 0.508 | |
snp.dprime-class | 0.069 | 0.004 | 0.074 | |
snp.lhs.tests | 0.098 | 0.000 | 0.099 | |
snp.matrix-class | 0.132 | 0.000 | 0.132 | |
snp.pre | 0.088 | 0.000 | 0.088 | |
snp.rhs.tests | 0.082 | 0.000 | 0.081 | |
testdata | 0.12 | 0.00 | 0.12 | |
xxt | 0.457 | 0.004 | 0.462 | |