David Clayton
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/snpStats |
| git_branch: devel |
| git_last_commit: 6be473e |
| git_last_commit_date: 2024-04-30 10:17:46 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:14 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 1955/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| snpStats 1.55.0 (landing page) David Clayton
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the snpStats package: - 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. |
| Package: snpStats |
| Version: 1.55.0 |
| 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_1.55.0.tar.gz |
| StartedAt: 2024-05-13 03:43:48 -0400 (Mon, 13 May 2024) |
| EndedAt: 2024-05-13 03:45:04 -0400 (Mon, 13 May 2024) |
| EllapsedTime: 76.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: snpStats.Rcheck |
| Warnings: 2 |
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### 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_1.55.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/snpStats.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snpStats/DESCRIPTION’ ... OK
* this is package ‘snpStats’ version ‘1.55.0’
* 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:568:7: 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-mac-arm64/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-mac-arm64/meat/snpStats.Rcheck/00check.log’
for details.
snpStats.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL snpStats
###
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* 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:568:7: warning: variable 'df_rV' is uninitialized when used here [-Wuninitialized]
Free(df_rV);
^~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:55:46: note: expanded from macro 'Free'
#define 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)
snpStats.Rcheck/snpStats-Ex.timings
| name | user | system | elapsed | |
| Fst | 0.832 | 0.029 | 0.878 | |
| GlmEstimates-class | 0.002 | 0.000 | 0.002 | |
| GlmTests-class | 0.001 | 0.001 | 0.001 | |
| ImputationRules-class | 0.001 | 0.000 | 0.001 | |
| SingleSnpTests-class | 0.000 | 0.001 | 0.001 | |
| SnpMatrix-class | 0.434 | 0.011 | 0.446 | |
| XSnpMatrix-class | 0.117 | 0.006 | 0.125 | |
| chi.squared | 0.107 | 0.004 | 0.112 | |
| families | 0.021 | 0.003 | 0.023 | |
| filter.rules | 0.000 | 0.000 | 0.001 | |
| for.exercise | 1.139 | 0.022 | 1.237 | |
| ibsCount | 0.280 | 0.005 | 0.288 | |
| ibsDist | 0.243 | 0.005 | 0.247 | |
| imputation.maf | 0.000 | 0.000 | 0.001 | |
| impute.snps | 0.902 | 0.020 | 0.930 | |
| ld | 0.112 | 0.005 | 0.116 | |
| mean2g | 0.111 | 0.005 | 0.116 | |
| misinherits | 0.046 | 0.025 | 0.072 | |
| mvtests | 0 | 0 | 0 | |
| plotUncertainty | 0 | 0 | 0 | |
| pool | 0.198 | 0.005 | 0.202 | |
| pp | 0.062 | 0.002 | 0.065 | |
| qq.chisq | 0 | 0 | 0 | |
| random.snps | 0.003 | 0.001 | 0.004 | |
| read.beagle | 0 | 0 | 0 | |
| read.impute | 0.000 | 0.000 | 0.001 | |
| read.long | 0 | 0 | 0 | |
| read.mach | 0 | 0 | 0 | |
| read.pedfile | 0 | 0 | 0 | |
| row.summary | 0.180 | 0.005 | 0.186 | |
| single.snp.tests | 0.128 | 0.007 | 0.135 | |
| sm.compare | 0.001 | 0.000 | 0.000 | |
| snp.cor | 0.386 | 0.006 | 0.392 | |
| snp.imputation | 0.894 | 0.038 | 0.933 | |
| snp.lhs.estimates | 0.224 | 0.027 | 0.251 | |
| snp.lhs.tests | 0.113 | 0.006 | 0.119 | |
| snp.pre.multiply | 0.122 | 0.004 | 0.126 | |
| snp.rhs.estimates | 0.139 | 0.014 | 0.156 | |
| snp.rhs.tests | 0.107 | 0.004 | 0.115 | |
| switch.alleles | 0.111 | 0.006 | 0.118 | |
| tdt.snp | 0.024 | 0.003 | 0.027 | |
| test.allele.switch | 0.157 | 0.009 | 0.167 | |
| testdata | 0.179 | 0.010 | 0.189 | |
| write.plink | 0.204 | 0.017 | 0.222 | |
| xxt | 0.328 | 0.008 | 0.337 | |