| Back to First build/check report with an "external build node" |
This page was generated on 2023-06-01 18:17:19 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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: 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 80/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| snpStats 1.51.0 (landing page) David Clayton
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | WARNINGS | ||||||||
| Package: snpStats |
| Version: 1.51.0 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings snpStats_1.51.0.tar.gz |
| StartedAt: 2023-06-01 13:25:07 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 13:28:31 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 204.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: snpStats.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings snpStats_1.51.0.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/snpStats.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘snpStats/DESCRIPTION’ ... OK
* this is package ‘snpStats’ version ‘1.51.0’
* 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 ‘snpStats’ can be installed ... WARNING
Found the following significant warnings:
input.c:788:5: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:442:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:440:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:438:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:435:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:432:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
input.c:429:11: warning: ‘__builtin_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 ‘/home/hpages/bbs-3.18-bioc-testing/meat/snpStats.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
* checking installed package size ... NOTE
installed size is 6.1Mb
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 loading without being on the library search path ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs/snpStats/libs/snpStats.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘rand’, possibly from ‘rand’ (C)
File ‘snpStats/libs/snpStats.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 ...
‘Fst-vignette.Rnw’... OK
‘data-input-vignette.Rnw’... OK
‘differences.Rnw’... OK
‘imputation-vignette.Rnw’... OK
‘ld-vignette.Rnw’... OK
‘pca-vignette.Rnw’... OK
‘snpStats-vignette.Rnw’... OK
‘tdt-vignette.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/hpages/bbs-3.18-bioc-testing/meat/snpStats.Rcheck/00check.log’
for details.
snpStats.Rcheck/00install.out
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### Running command:
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### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL snpStats
###
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* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* installing *source* package ‘snpStats’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Runcertain.c -o Runcertain.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bind.c -o bind.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_gt.c -o count_gt.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c covwin.c -o covwin.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fst.c -o fst.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_test.c -o glm_test.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hphase.c -o hphase.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imputation.c -o imputation.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c in.c -o in.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c input.c -o input.o
input.c: In function ‘simplify_names’:
input.c:788:5: warning: ‘__builtin_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:442:11: warning: ‘__builtin_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:440:11: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
440 | strncpy(gtype1, field, MAX_FLD-1);
| ^
input.c:438:11: warning: ‘__builtin_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:435:11: warning: ‘__builtin_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:432:11: warning: ‘__builtin_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:429:11: warning: ‘__builtin_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"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c invert.c -o invert.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ipf.c -o ipf.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ld.c -o ld.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c misc.c -o misc.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mla.c -o mla.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mvphenotype.c -o mvphenotype.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c outdata.c -o outdata.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plink.c -o plink.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c read_uncertain.c -o read_uncertain.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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);
| ^~
In file included from /usr/include/stdio.h:906,
from /home/hpages/bbs-3.18-bioc/R/include/R.h:44,
from readped.c:3:
In function ‘snprintf’,
inlined from ‘readped’ at readped.c:234:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: note: ‘__builtin___snprintf_chk’ output between 3 and 140 bytes into a destination of size 128
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
single_snp_tests.c: In function ‘score_single’:
single_snp_tests.c:223:11: warning: ‘name_index’ may be used uninitialized [-Wmaybe-uninitialized]
223 | do_impute(Snps, n, NULL, subset, nsubj, name_index, Rule, gt2ht,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | xadd, xdom);
| ~~~~~~~~~~~
single_snp_tests.c:108:12: note: ‘name_index’ was declared here
108 | index_db name_index;
| ^~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c structure.c -o structure.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subset.c -o subset.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tdt.c -o tdt.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:906,
from /home/hpages/bbs-3.18-bioc/R/include/R.h:44,
from testBig.c:1:
In function ‘sprintf’,
inlined from ‘snp_big’ at testBig.c:31:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 18 bytes into a destination of size 16
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uncertain.c -o uncertain.o
gcc -shared -L/usr/local/lib -o snpStats.so 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 -lz
installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/00LOCK-snpStats/00new/snpStats/libs
** 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
** 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 (snpStats)
snpStats.Rcheck/snpStats-Ex.timings
| name | user | system | elapsed | |
| Fst | 0.680 | 0.024 | 0.704 | |
| GlmEstimates-class | 0.001 | 0.000 | 0.001 | |
| GlmTests-class | 0 | 0 | 0 | |
| ImputationRules-class | 0 | 0 | 0 | |
| SingleSnpTests-class | 0.001 | 0.000 | 0.000 | |
| SnpMatrix-class | 0.227 | 0.011 | 0.239 | |
| XSnpMatrix-class | 0.132 | 0.016 | 0.149 | |
| chi.squared | 0.104 | 0.012 | 0.128 | |
| families | 0.018 | 0.003 | 0.022 | |
| filter.rules | 0 | 0 | 0 | |
| for.exercise | 1.397 | 0.033 | 1.428 | |
| ibsCount | 0.515 | 0.016 | 0.530 | |
| ibsDist | 0.301 | 0.004 | 0.305 | |
| imputation.maf | 0 | 0 | 0 | |
| impute.snps | 0.751 | 0.015 | 0.768 | |
| ld | 0.104 | 0.000 | 0.104 | |
| mean2g | 0.106 | 0.000 | 0.106 | |
| misinherits | 0.037 | 0.008 | 0.044 | |
| mvtests | 0 | 0 | 0 | |
| plotUncertainty | 0 | 0 | 0 | |
| pool | 0.256 | 0.000 | 0.256 | |
| pp | 0.087 | 0.000 | 0.099 | |
| qq.chisq | 0.001 | 0.000 | 0.000 | |
| random.snps | 0.005 | 0.000 | 0.005 | |
| read.beagle | 0 | 0 | 0 | |
| read.impute | 0.001 | 0.000 | 0.000 | |
| read.long | 0 | 0 | 0 | |
| read.mach | 0 | 0 | 0 | |
| read.pedfile | 0.000 | 0.001 | 0.001 | |
| row.summary | 0.183 | 0.006 | 0.189 | |
| single.snp.tests | 0.142 | 0.004 | 0.146 | |
| sm.compare | 0 | 0 | 0 | |
| snp.cor | 0.629 | 0.011 | 0.641 | |
| snp.imputation | 0.77 | 0.02 | 0.79 | |
| snp.lhs.estimates | 0.202 | 0.016 | 0.218 | |
| snp.lhs.tests | 0.107 | 0.009 | 0.116 | |
| snp.pre.multiply | 0.108 | 0.015 | 0.123 | |
| snp.rhs.estimates | 0.131 | 0.004 | 0.135 | |
| snp.rhs.tests | 0.100 | 0.008 | 0.109 | |
| switch.alleles | 0.108 | 0.004 | 0.113 | |
| tdt.snp | 0.022 | 0.000 | 0.022 | |
| test.allele.switch | 0.144 | 0.000 | 0.143 | |
| testdata | 0.166 | 0.008 | 0.174 | |
| write.plink | 0.141 | 0.000 | 0.140 | |
| xxt | 0.382 | 0.000 | 0.381 | |