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This page was generated on 2023-04-12 11:05:20 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (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

CHECK results for snpStats on nebbiolo2


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.

raw results

Package 1912/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snpStats 1.48.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: snpStats
Version: 1.48.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings snpStats_1.48.0.tar.gz
StartedAt: 2023-04-11 00:10:04 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:13:00 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 175.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: snpStats.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings snpStats_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/snpStats.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘snpStats’ can be installed ... WARNING
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: 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/biocbuild/bbs-3.16-bioc/meat/snpStats.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.4Mb
  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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/snpStats/libs/snpStats.so’:
  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. 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/snpStats.Rcheck/00check.log’
for details.



Installation output

snpStats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL snpStats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘snpStats’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Runcertain.c -o Runcertain.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c count_gt.c -o count_gt.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c covwin.c -o covwin.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c force_hom.c -o force_hom.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fst.c -o fst.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c glm_test.c -o glm_test.o
gcc -I"/home/biocbuild/bbs-3.16-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/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hash_index.c -o hash_index.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hphase.c -o hphase.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c imputation.c -o imputation.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c in.c -o in.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c input.c -o input.o
In file included from /usr/include/string.h:495,
                 from input.c:6:
In function ‘strncpy’,
    inlined from ‘simplify_names’ at input.c:788:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘insnp_new’ at input.c:442:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘insnp_new’ at input.c:438:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘insnp_new’ at input.c:435:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘insnp_new’ at input.c:432:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘insnp_new’ at input.c:429:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c invert.c -o invert.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ipf.c -o ipf.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ld.c -o ld.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c misc.c -o misc.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mla.c -o mla.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mvphenotype.c -o mvphenotype.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c outdata.c -o outdata.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c plink.c -o plink.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c read_uncertain.c -o read_uncertain.o
gcc -I"/home/biocbuild/bbs-3.16-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:867,
                 from /home/biocbuild/bbs-3.16-bioc/R/include/R.h:45,
                 from readped.c:3:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 3 and 140 bytes into a destination of size 128
   67 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   68 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-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:223:4: 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"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c snp_summary.c -o snp_summary.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c snpmpy.c -o snpmpy.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c solve_cubic.c -o solve_cubic.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c structure.c -o structure.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c subset.c -o subset.o
gcc -I"/home/biocbuild/bbs-3.16-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/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c tdt.c -o tdt.o
gcc -I"/home/biocbuild/bbs-3.16-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:867,
                 from /home/biocbuild/bbs-3.16-bioc/R/include/R.h:45,
                 from testBig.c:1:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 9 and 18 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c uncertain.c -o uncertain.o
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -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 -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/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)

Tests output


Example timings

snpStats.Rcheck/snpStats-Ex.timings

nameusersystemelapsed
Fst0.4920.0280.520
GlmEstimates-class0.0010.0000.001
GlmTests-class0.0010.0000.000
ImputationRules-class000
SingleSnpTests-class0.0000.0000.001
SnpMatrix-class0.1510.0200.172
XSnpMatrix-class0.0780.0080.087
chi.squared0.0750.0000.074
families0.0180.0000.017
filter.rules000
for.exercise1.1160.0081.125
ibsCount0.4130.0080.421
ibsDist0.2600.0080.268
imputation.maf0.0010.0000.000
impute.snps0.6530.0440.697
ld0.0720.0040.075
mean2g0.0730.0040.077
misinherits0.0360.0070.045
mvtests000
plotUncertainty0.0010.0000.000
pool0.1520.0000.152
pp0.0610.0000.074
qq.chisq000
random.snps0.0030.0000.003
read.beagle000
read.impute000
read.long000
read.mach0.0000.0000.001
read.pedfile000
row.summary0.1100.0080.119
single.snp.tests0.0880.0040.092
sm.compare000
snp.cor0.3900.0030.393
snp.imputation0.6310.0320.663
snp.lhs.estimates0.1750.0050.179
snp.lhs.tests0.0780.0040.081
snp.pre.multiply0.0760.0120.088
snp.rhs.estimates0.0950.0120.107
snp.rhs.tests0.0690.0080.077
switch.alleles0.0840.0060.090
tdt.snp0.0330.0000.033
test.allele.switch0.0970.0070.105
testdata0.1290.0050.133
write.plink0.1240.0000.124
xxt0.3210.0040.325