| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:28 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 330/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chopsticks 1.67.0 (landing page) Hin-Tak Leung
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: chopsticks |
| Version: 1.67.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:chopsticks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings chopsticks_1.67.0.tar.gz |
| StartedAt: 2023-06-05 19:24:49 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 19:26:12 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 83.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: chopsticks.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:chopsticks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings chopsticks_1.67.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/chopsticks.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘chopsticks’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 5.8Mb
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 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 loading without being on the library search path ... OK
* checking 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
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
prepare_Rd: read.wtccc.signals.Rd:58: Dropping empty section \seealso
checkRd: (-1) read.wtccc.signals.Rd:30: Escaped LaTeX specials: \_ \_
checkRd: (-1) snpMatrix-package.Rd:21: Escaped LaTeX specials: \_ \_
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 ... 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 ... 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-4.3.0/site-library/chopsticks/libs/chopsticks.so’:
Found ‘sprintf’, possibly from ‘sprintf’ (C)
File ‘chopsticks/libs/chopsticks.so’:
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 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 ...
‘chopsticks-vignette.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/chopsticks.Rcheck/00check.log’
for details.
chopsticks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL chopsticks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘chopsticks’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c adler32.c -o adler32.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c bind.c -o bind.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c compress.c -o compress.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c crc32.c -o crc32.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c deflate.c -o deflate.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c force_hom.c -o force_hom.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test.c -o glm_test.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test_R.c -o glm_test_R.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c gzio.c -o gzio.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hash_index.c -o hash_index.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ibs.c -o ibs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c in.c -o in.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c infback.c -o infback.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inffast.c -o inffast.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inflate.c -o inflate.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inftrees.c -o inftrees.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c input.c -o input.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inputNew.c -o inputNew.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c input_unsorted.c -o input_unsorted.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ld_graphic_eps.c -o ld_graphic_eps.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ld_with.c -o ld_with.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mla.c -o mla.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c outdata.c -o outdata.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pairwise_linkage.c -o pairwise_linkage.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_chiamo.c -o read_chiamo.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_hapmap.c -o read_hapmap.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_pedfile.c -o read_pedfile.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_signals.c -o read_signals.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c readped.c -o readped.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c sdfpw.c -o sdfpw.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c single_snp_tests.c -o single_snp_tests.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snp_summary.c -o snp_summary.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snpmpy.c -o snpmpy.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c solve_cubic.c -o solve_cubic.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c solve_quadratic.c -o solve_quadratic.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c structure.c -o structure.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c trees.c -o trees.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c uncompr.c -o uncompr.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c zutil.c -o zutil.o gcc -shared -L/home/biocbuild/R/R-4.3.0/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-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 | 0.089 | 0.011 | 0.101 | |
| X.snp.matrix-class | 0.076 | 0.004 | 0.080 | |
| epsout.ld.snp | 0.111 | 0.004 | 0.115 | |
| for.exercise | 0.657 | 0.016 | 0.675 | |
| ibs.stats | 0.278 | 0.024 | 0.303 | |
| ibsCount | 0.145 | 0.008 | 0.153 | |
| ibsDist | 0.116 | 0.000 | 0.116 | |
| ld.snp | 0.108 | 0.000 | 0.108 | |
| ld.with | 0.083 | 0.000 | 0.083 | |
| pair.result.ld.snp | 0.071 | 0.004 | 0.075 | |
| plot.snp.dprime | 0.182 | 0.008 | 0.190 | |
| 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 | 0.093 | 0.000 | 0.093 | |
| single.snp.tests | 0.098 | 0.000 | 0.098 | |
| snp-class | 0 | 0 | 0 | |
| snp.cbind | 0.186 | 0.004 | 0.190 | |
| snp.cor | 0.509 | 0.000 | 0.509 | |
| snp.dprime-class | 0.073 | 0.000 | 0.073 | |
| snp.lhs.tests | 0.099 | 0.000 | 0.099 | |
| snp.matrix-class | 0.130 | 0.001 | 0.133 | |
| snp.pre | 0.085 | 0.004 | 0.089 | |
| snp.rhs.tests | 0.082 | 0.000 | 0.082 | |
| testdata | 0.123 | 0.000 | 0.123 | |
| xxt | 0.460 | 0.000 | 0.462 | |