Comments (3)
zkamvar
commented on June 13, 2024
If you're interested, here's what went on when I was attempting to find a memory leak in my own code: grunwaldlab/poppr#40
I also have a build of R-devel with valgrind enabled: https://github.com/grunwaldlab/poppr/wiki/R-CMD-check-with-docker-rocker
My experience installing R with valgrind has been frustrating, even on Ubuntu. Docker can still be frustrating, but it's not as frustrating as trying to compile R from source.
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zkamvar
commented on June 13, 2024
Valgrind reports:
vcf functions: ......................==18546== Conditional jump or move depends on uninitialised value(s)
==18546== at 0x30750046DC: deflate (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x307500DDFC: ??? (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x307500E685: gzclose_w (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x1139582A: write_vcf_body(Rcpp::Matrix<16, Rcpp::PreserveStorage>, Rcpp::Matrix<16, Rcpp::PreserveStorage>, std::string, int) (packages/tests-vg/vcfR/src/vcf_io.cpp:555)
==18546== by 0x11374EB8: vcfR_write_vcf_body (packages/tests-vg/vcfR/src/RcppExports.cpp:263)
==18546== by 0x47AFAD: do_dotcall (svn/R-devel/src/main/dotcode.c:1252)
==18546== by 0x4B1039: Rf_eval (svn/R-devel/src/main/eval.c:713)
==18546== by 0x4B446D: do_set (svn/R-devel/src/main/eval.c:2211)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B3418: do_begin (svn/R-devel/src/main/eval.c:1821)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== Uninitialised value was created by a heap allocation
==18546== at 0x4A06C50: malloc (in /usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so)
==18546== by 0x307500CA69: ??? (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x113952B9: write_vcf_body(Rcpp::Matrix<16, Rcpp::PreserveStorage>, Rcpp::Matrix<16, Rcpp::PreserveStorage>, std::string, int) (packages/tests-vg/vcfR/src/vcf_io.cpp:520)
==18546== by 0x11374EB8: vcfR_write_vcf_body (packages/tests-vg/vcfR/src/RcppExports.cpp:263)
==18546== by 0x47AFAD: do_dotcall (svn/R-devel/src/main/dotcode.c:1252)
==18546== by 0x4B1039: Rf_eval (svn/R-devel/src/main/eval.c:713)
==18546== by 0x4B446D: do_set (svn/R-devel/src/main/eval.c:2211)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B3418: do_begin (svn/R-devel/src/main/eval.c:1821)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B3418: do_begin (svn/R-devel/src/main/eval.c:1821)
==18546==
==18546== Conditional jump or move depends on uninitialised value(s)
==18546== at 0x30750046DC: deflate (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x307500DE56: ??? (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x307500E685: gzclose_w (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x1139582A: write_vcf_body(Rcpp::Matrix<16, Rcpp::PreserveStorage>, Rcpp::Matrix<16, Rcpp::PreserveStorage>, std::string, int) (packages/tests-vg/vcfR/src/vcf_io.cpp:555)
==18546== by 0x11374EB8: vcfR_write_vcf_body (packages/tests-vg/vcfR/src/RcppExports.cpp:263)
==18546== by 0x47AFAD: do_dotcall (svn/R-devel/src/main/dotcode.c:1252)
==18546== by 0x4B1039: Rf_eval (svn/R-devel/src/main/eval.c:713)
==18546== by 0x4B446D: do_set (svn/R-devel/src/main/eval.c:2211)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B3418: do_begin (svn/R-devel/src/main/eval.c:1821)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== Uninitialised value was created by a heap allocation
==18546== at 0x4A06C50: malloc (in /usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so)
==18546== by 0x307500CA69: ??? (in /usr/lib64/libz.so.1.2.8)
==18546== by 0x113952B9: write_vcf_body(Rcpp::Matrix<16, Rcpp::PreserveStorage>, Rcpp::Matrix<16, Rcpp::PreserveStorage>, std::string, int) (packages/tests-vg/vcfR/src/vcf_io.cpp:520)
==18546== by 0x11374EB8: vcfR_write_vcf_body (packages/tests-vg/vcfR/src/RcppExports.cpp:263)
==18546== by 0x47AFAD: do_dotcall (svn/R-devel/src/main/dotcode.c:1252)
==18546== by 0x4B1039: Rf_eval (svn/R-devel/src/main/eval.c:713)
==18546== by 0x4B446D: do_set (svn/R-devel/src/main/eval.c:2211)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B3418: do_begin (svn/R-devel/src/main/eval.c:1821)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B0E90: Rf_eval (svn/R-devel/src/main/eval.c:685)
==18546== by 0x4B3418: do_begin (svn/R-devel/src/main/eval.c:1821)
==18546==
When you look at lines 520 and 555 in the code, you see a gzFile being created. I notice that there's another gzFile opened here: https://github.com/knausb/vcfR/blob/v1.2.0/src/vcf_io.cpp#L47, but it's being initialized before gzopen is being called.
I wonder if this could be fixed by separating the declaration from the function:
gzFile fi;
fi = gzopen( filename.c_str(), "ab" );
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knausb
commented on June 13, 2024
I think I addressed this a while ago. Thanks @zkamvar for your help and ideas! I'm slowly becoming better with Docker.
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Related Issues (20)
- Variants with MAF of 0 after removing monomorphics HOT 6
- Error: ID column contains non-unique names HOT 1
- How can I add population information to genind converted using vcfR2genind? HOT 2
- RStudio Session aborted when writing VCF
- vcfR not recognizing all chromosomes HOT 2
- Heterozygous SNP calling HOT 15
- read.vcfR() coredump with empty lines in input HOT 5
- Rename Genotype information HOT 2
- vcfR2tidy can't handle files with empty INFO HOT 4
- gene/chromosome annotation HOT 2
- write.vcf() not filtering variants HOT 2
- Filtering for minor allele Frequency HOT 4
- Assign_Indiv_by_Geno.R function of Demuxafy.sif problems with the vcf HOT 1
- chromR object not finding DP and MQ values HOT 2
- read.vcfR() not recognizing missing data HOT 3
- extract.gt() missing heterozygotes HOT 1
- compilation issue HOT 2
- Hide a panel from chromoqc or plot HOT 2
- vcfR Subsetting to the first chromosome HOT 1
- change genotype(change gap to NA) HOT 2
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