Some failures in tests [ FAIL 13 | WARN 0 | SKIP 1 | PASS 174 ]

[barracuda156]

--->  Testing R-bigsnpr
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/bigsnpr" && /opt/local/bin/R CMD check ./bigsnpr_1.12.15.tar.gz --no-manual --no-build-vignettes 
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/bigsnpr/bigsnpr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
    gcc-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
    GNU Fortran (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘bigsnpr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigsnpr’ version ‘1.12.15’
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bigsnpr’ can be installed ... OK
* used C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0’
* used SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
* checking installed package size ... OK
* checking package 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 ... 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 LazyData ... 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 ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
  Backtrace:
      ▆
   1. ├─bigsnpr::snp_attach(...) at test-1-readBGEN.R:150:3
   2. │ └─bigassertr::assert_exist(rdsfile)
   3. │   └─base::file.exists(file)
   4. └─bigsnpr::snp_readBGEN(...)
   5.   └─base::sapply(bgenfiles, check_bgen_format)
   6.     └─base::lapply(X = X, FUN = FUN, ...)
   7.       └─bigsnpr (local) FUN(X[[i]], ...)
   8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)

  [ FAIL 13 | WARN 0 | SKIP 1 | PASS 174 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)

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> library(testthat)
> library(bigsnpr)
Loading required package: bigstatsr
> 
> for (k in 1:9)
+   test_check("bigsnpr", filter = paste0(k, '-'))
[ FAIL 13 | WARN 0 | SKIP 1 | PASS 174 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• is_cran is TRUE (1): 'test-1-readBed.R:53:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-1-prodBGEN.R:37:3'): same as with intermediate FBM ─────────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de170e79847.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─... %>% .$genotypes at test-1-prodBGEN.R:37:3
 2. ├─bigsnpr::snp_attach(.)
 3. │ └─bigassertr::assert_exist(rdsfile)
 4. │   └─base::file.exists(file)
 5. └─bigsnpr::snp_readBGEN(bgen_file, tempfile(), list(IDs), ncores = ncores())
 6.   └─base::sapply(bgenfiles, check_bgen_format)
 7.     └─base::lapply(X = X, FUN = FUN, ...)
 8.       └─bigsnpr (local) FUN(X[[i]], ...)
 9.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-prodBGEN.R:69:3'): works with a subset of SNPs ───────────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de170e79847.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-prodBGEN.R:69:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(...)
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-prodBGEN.R:81:3'): works with a subset of individuals ────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de170e79847.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-prodBGEN.R:81:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(...)
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-prodBGEN.R:97:3'): works with multiple files ─────────────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de170e79847.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-prodBGEN.R:97:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(...)
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Failure ('test-1-readBGEN.R:40:3'): raises some errors ──────────────────────
`snp_attach(...)` threw an error with unexpected message.
Expected match: "Wrong format of some variants."
Actual message: "'/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib."
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-1-readBGEN.R:40:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─bigsnpr::snp_attach(...)
  7. │ └─bigassertr::assert_exist(rdsfile)
  8. │   └─base::file.exists(file)
  9. └─bigsnpr::snp_readBGEN(...)
 10.   └─base::sapply(bgenfiles, check_bgen_format)
 11.     └─base::lapply(X = X, FUN = FUN, ...)
 12.       └─bigsnpr (local) FUN(X[[i]], ...)
 13.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-readBGEN.R:59:5'): same as package {rbgen} ───────────────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
Backtrace:
     ▆
  1. └─base::replicate(...) at test-1-readBGEN.R:58:3
  2.   └─base::sapply(...)
  3.     └─base::lapply(X = X, FUN = FUN, ...)
  4.       └─bigsnpr (local) FUN(X[[i]], ...)
  5.         ├─bigsnpr::snp_attach(...) at test-1-readBGEN.R:59:5
  6.         │ └─bigassertr::assert_exist(rdsfile)
  7.         │   └─base::file.exists(file)
  8.         └─bigsnpr::snp_readBGEN(bgen_file, tempfile(), list(IDs), ncores = ncores())
  9.           └─base::sapply(bgenfiles, check_bgen_format)
 10.             └─base::lapply(X = X, FUN = FUN, ...)
 11.               └─bigsnpr (local) FUN(X[[i]], ...)
 12.                 └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-readBGEN.R:71:3'): same variant infos as with QCTOOL ─────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-readBGEN.R:71:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(bgen_file, tempfile(), list(IDs), ncores = ncores())
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-readBGEN.R:92:3'): works with a subset of SNPs ───────────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-readBGEN.R:92:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(...)
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Failure ('test-1-readBGEN.R:102:3'): works with a subset of individuals ─────
`snp_readBGEN(...)` threw an error with unexpected message.
Expected match: "all(ind_row >= 1 & ind_row <= N) is not TRUE"
Actual message: "'/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib."
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-1-readBGEN.R:102:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─bigsnpr::snp_readBGEN(...)
  7.   └─base::sapply(bgenfiles, check_bgen_format)
  8.     └─base::lapply(X = X, FUN = FUN, ...)
  9.       └─bigsnpr (local) FUN(X[[i]], ...)
 10.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-readBGEN.R:106:3'): works with a subset of individuals ───────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-readBGEN.R:106:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(...)
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-readBGEN.R:120:3'): works with multiple files ────────────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-readBGEN.R:120:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(...)
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-readBGEN.R:132:3'): read as random hard calls ────────────────
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(snp_readBGEN(bgen_file, tempfile(), list(IDs))) at test-1-readBGEN.R:132:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(bgen_file, tempfile(), list(IDs))
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)
── Error ('test-1-readBGEN.R:150:3'): work with duplicated variants or individuals ──
Error: '/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-bigsnpr/R-bigsnpr/work/.tmp/RtmpVGyuXc/file10de11cf92790.bgen' is not compressed with zlib.
Backtrace:
    ▆
 1. ├─bigsnpr::snp_attach(...) at test-1-readBGEN.R:150:3
 2. │ └─bigassertr::assert_exist(rdsfile)
 3. │   └─base::file.exists(file)
 4. └─bigsnpr::snp_readBGEN(...)
 5.   └─base::sapply(bgenfiles, check_bgen_format)
 6.     └─base::lapply(X = X, FUN = FUN, ...)
 7.       └─bigsnpr (local) FUN(X[[i]], ...)
 8.         └─bigassertr::stop2("'%s' is not compressed with zlib.", bgenfile)

[ FAIL 13 | WARN 0 | SKIP 1 | PASS 174 ]
Error: Test failures
Execution halted

[privefl]

Is it some old Mac using 32 bits? I thought 32 bit was deprecated for R?

[barracuda156]

@privefl Thank you for responding. R upstream does not test on 32-bit and does not actively maintain it, but it works. In MacPorts I support at least 32-bit PowerPC (i386 is not tested regularly). I think R should also work on 32-bit BSD and Linux, though I have no environment to try that.

[privefl]

The error seems to be with the BGEN format. What do you want me to do about it? Can you use 64bit instead?

[barracuda156]

@privefl If you could suggest how to try fixing that, I will test locally. (This is not something I can fix myself, I don’t know what exactly this does.)

If you could test this on your end, Linux supports 32-bit, including big-endian ppc.

[privefl]

Just want to make sure whether this is really needed; can't you switch R to use 64 bit instead?