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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2001/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snpStats 1.56.0  (landing page)
David Clayton
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/snpStats
git_branch: RELEASE_3_20
git_last_commit: 92d244d
git_last_commit_date: 2024-10-29 09:28:44 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for snpStats on kjohnson1

To the developers/maintainers of the snpStats package:
- 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 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.

raw results


Summary

Package: snpStats
Version: 1.56.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:snpStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings snpStats_1.56.0.tar.gz
StartedAt: 2024-12-21 09:58:29 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 09:59:47 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 78.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: snpStats.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:snpStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings snpStats_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/snpStats.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snpStats/DESCRIPTION’ ... OK
* this is package ‘snpStats’ version ‘1.56.0’
* 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:
  bind.c:243:89: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
  glm_test_R.c:305:56: warning: data argument not used by format string [-Wformat-extra-args]
  glm_test_R.c:805:56: warning: data argument not used by format string [-Wformat-extra-args]
  glm_test_R.c:937:63: warning: data argument not used by format string [-Wformat-extra-args]
  mvphenotype.c:568:9: warning: variable 'df_rV' is uninitialized when used here [-Wuninitialized]
  read_uncertain.c:103:62: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/snpStats.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  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 ... OK
* 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 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) glm.test.control.Rd:28-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glm.test.control.Rd:32-34: Lost braces in \itemize; meant \describe ?
* 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 ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/snpStats.Rcheck/00check.log’
for details.


Installation output

snpStats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL snpStats
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘snpStats’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Runcertain.c -o Runcertain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bind.c -o bind.o
bind.c:243:89: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
              error("Duplicated column name at column %d overall from column %d of object %d", ij+1, j+1, i+1);
                                                      ~~                                       ^~~~
                                                      %td
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_gt.c -o count_gt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c covwin.c -o covwin.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c force_hom.c -o force_hom.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fst.c -o fst.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c glm_test.c -o glm_test.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c glm_test_R.c -o glm_test_R.o
glm_test_R.c:305:56: warning: data argument not used by format string [-Wformat-extra-args]
        warning("Matrix not positive semi-definite in test ", t+1);
                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ^
glm_test_R.c:805:56: warning: data argument not used by format string [-Wformat-extra-args]
        warning("Matrix not positive semi-definite in test ", test+1);
                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ^
glm_test_R.c:368:7: warning: unused variable 'max_name_length' [-Wunused-variable]
  int max_name_length =  MAX_NAME_LENGTH -1;
      ^
glm_test_R.c:937:63: warning: data argument not used by format string [-Wformat-extra-args]
        warning("Matrix not positive semi-definite in pooled test ", i+1);
                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hash_index.c -o hash_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hphase.c -o hphase.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c imputation.c -o imputation.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c in.c -o in.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c input.c -o input.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c invert.c -o invert.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ipf.c -o ipf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ld.c -o ld.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c misc.c -o misc.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mla.c -o mla.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mvphenotype.c -o mvphenotype.o
mvphenotype.c:568:9: warning: variable 'df_rV' is uninitialized when used here [-Wuninitialized]
        R_Free(df_rV);
               ^~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:60:46: note: expanded from macro 'R_Free'
#define R_Free(p)      (R_chk_free( (void *)(p) ), (p) = NULL)
                                             ^
mvphenotype.c:486:20: note: initialize the variable 'df_rV' to silence this warning
      double *df_rV; 
                   ^
                    = NULL
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c outdata.c -o outdata.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c plink.c -o plink.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c read_uncertain.c -o read_uncertain.o
read_uncertain.c:103:62: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  Rprintf("Reading SnpMatrix with %d rows and %d columns\n", lines, ncol);
                                  ~~                         ^~~~~
                                  %ld
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c readped.c -o readped.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c single_snp_tests.c -o single_snp_tests.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snp_summary.c -o snp_summary.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snpmpy.c -o snpmpy.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c solve_cubic.c -o solve_cubic.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c structure.c -o structure.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c subset.c -o subset.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c switch.c -o switch.o
switch.c:32:8: warning: variable 'female2' set but not used [-Wunused-but-set-variable]
  int *female2 = NULL;
       ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tdt.c -o tdt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c testBig.c -o testBig.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c uncertain.c -o uncertain.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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
Fst0.8400.0280.870
GlmEstimates-class0.0020.0010.001
GlmTests-class0.0010.0010.002
ImputationRules-class000
SingleSnpTests-class0.0000.0000.001
SnpMatrix-class0.4450.0110.457
XSnpMatrix-class0.1180.0050.125
chi.squared0.1080.0040.112
families0.0210.0020.024
filter.rules000
for.exercise1.3870.0231.410
ibsCount0.3420.0050.347
ibsDist0.2490.0060.254
imputation.maf000
impute.snps0.8710.0230.900
ld0.1120.0040.116
mean2g0.1090.0040.114
misinherits0.0460.0250.070
mvtests000
plotUncertainty000
pool0.1990.0060.205
pp0.0620.0030.065
qq.chisq000
random.snps0.0040.0000.004
read.beagle000
read.impute000
read.long000
read.mach0.0000.0000.001
read.pedfile000
row.summary0.1780.0060.184
single.snp.tests0.1290.0070.137
sm.compare000
snp.cor0.3860.0060.392
snp.imputation0.8850.0310.916
snp.lhs.estimates0.2280.0250.254
snp.lhs.tests0.1160.0040.121
snp.pre.multiply0.1250.0050.131
snp.rhs.estimates0.1390.0120.152
snp.rhs.tests0.1090.0040.113
switch.alleles0.1090.0050.115
tdt.snp0.0240.0040.027
test.allele.switch0.1570.0090.166
testdata0.1870.0100.197
write.plink0.2080.0170.225
xxt0.3240.0100.335