vcswatch reports that
this package seems to have new commits in its VCS but has
not yet updated debian/changelog. You should consider updating
the Debian changelog and uploading this new version into the archive.
Here are the relevant commit logs:
commit 50badf3338741e739b2bb591a8930d177fa6de6c
Author: Nilesh Patra <nilesh@debian.org>
Date: Sun Jul 31 18:49:33 2022 +0000
Attempt building on more archs
It doesn't seem to work on arm64 as of yet, log below.
Don't know why it triggers bolt again, but * sigh *
./bolt \
--bfile=EUR_subset \
--phenoFile=EUR_subset.pheno2.covars \
--exclude=EUR_subset.exclude2 \
--phenoCol=PHENO \
--phenoCol=QCOV1 \
--modelSnps=EUR_subset.modelSnps2 \
--reml \
--numThreads=2
+-----------------------------+
| ___ |
| BOLT-LMM, v2.3.6 /_ / |
| October 29, 2021 /_/ |
| Po-Ru Loh // |
| / |
+-----------------------------+
Copyright (C) 2014-2021 Harvard University.
Distributed under the GNU GPLv3 open source license.
Boost version: 1_74
Command line options:
./bolt \
--bfile=EUR_subset \
--phenoFile=EUR_subset.pheno2.covars \
--exclude=EUR_subset.exclude2 \
--phenoCol=PHENO \
--phenoCol=QCOV1 \
--modelSnps=EUR_subset.modelSnps2 \
--reml \
--numThreads=2
Setting number of threads to 2
fam: EUR_subset.fam
bim(s): EUR_subset.bim
bed(s): EUR_subset.bed
=== Reading genotype data ===
Total indivs in PLINK data: Nbed = 379
Total indivs stored in memory: N = 379
Reading bim file #1: EUR_subset.bim
Read 54051 snps
Total snps in PLINK data: Mbed = 54051
Reading exclude file (SNPs to exclude): EUR_subset.exclude2
Excluded 47959 SNP(s)
Reading list of SNPs to include in model (i.e., GRM): EUR_subset.modelSnps2
WARNING: SNP has been excluded: rs2176153
WARNING: SNP has been excluded: rs77036651
WARNING: SNP has been excluded: rs189917831
WARNING: SNP has been excluded: rs76452819
WARNING: SNP has been excluded: rs77203822
Included 1331 SNP(s) in model in 2 variance component(s)
WARNING: 10420 SNP(s) had been excluded
Breakdown of SNP pre-filtering results:
1331 SNPs to include in model (i.e., GRM)
0 additional non-GRM SNPs loaded
52720 excluded SNPs
Allocating 1331 x 380/4 bytes to store genotypes
Reading genotypes and performing QC filtering on snps and indivs...
Reading bed file #1: EUR_subset.bed
Expecting 5134845 (+3) bytes for 379 indivs, 54051 snps
Total indivs after QC: 379
Total post-QC SNPs: M = 1331
Variance component 1: 660 post-QC SNPs (name: 'chr21')
Variance component 2: 671 post-QC SNPs (name: 'chr22')
Time for SnpData setup = 0.630153 sec
=== Reading phenotype and covariate data ===
Read data for 373 indivs (ignored 0 without genotypes) from:
EUR_subset.pheno2.covars
Number of indivs with no missing phenotype(s) to use: 369
NOTE: Using all-1s vector (constant term) in addition to specified covariates
Using quantitative covariate: CONST_ALL_ONES
Number of individuals used in analysis: Nused = 369
Singular values of covariate matrix:
S[0] = 19.2094
Total covariate vectors: C = 1
Total independent covariate vectors: Cindep = 1
=== Initializing Bolt object: projecting and normalizing SNPs ===
Number of chroms with >= 1 good SNP: 2
Average norm of projected SNPs: 368.000000
Dimension of all-1s proj space (Nused-1): 368
Time for covariate data setup + Bolt initialization = 0.0125201 sec
Phenotype 1: N = 369 mean = -0.000706532 std = 1.02606
Phenotype 2: N = 369 mean = 1.53117 std = 0.499705
=== Estimating variance parameters ===
=== Making initial guesses for phenotype 1 ===
Using 3 random trials
+-----------------------------+
| ___ |
| BOLT-LMM, v2.3.6 /_ / |
| October 29, 2021 /_/ |
| Po-Ru Loh // |
| / |
+-----------------------------+
Copyright (C) 2014-2021 Harvard University.
Distributed under the GNU GPLv3 open source license.
Boost version: 1_74
Command line options:
(null)
ERROR: Use exactly one of the --bfile, --bfilegz, or --fam,bim,bed input formats
Aborting due to error processing command line arguments
For list of arguments, run with -h (--help) option
![[bug history graph]](https://qa.debian.org/data/bts/graphs/b/bolt-lmm.png){kind=link}