I used the previous implemented parameter for mzPntrs to allow stored mz objects to be used.
DrawAlignR passes an mzPntrs object to DIAlignR.
Adjusted tests where necessary, all tests passed.
==> Rcpp::compileAttributes()
* Updated R/RcppExports.R
==> devtools::check(document = FALSE)
── Building ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── DIAlignR ──
Setting env vars:
● CFLAGS : -Wall -pedantic -fdiagnostics-color=always
● CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always
● CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✓ checking for file ‘/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/DIAlignR/DESCRIPTION’ ...
─ preparing ‘DIAlignR’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to build vignettes
✓ creating vignettes (40.2s)
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘DIAlignR_0.99.9.tar.gz’
── Checking ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── DIAlignR ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
● _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
● _R_CHECK_CRAN_INCOMING_ : FALSE
● _R_CHECK_FORCE_SUGGESTS_ : FALSE
── R CMD check ─────────────────────────────────────────────────────────────────
─ using log directory ‘/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/DIAlignR.Rcheck’
─ using R version 3.6.1 (2019-07-05)
─ using platform: x86_64-pc-linux-gnu (64-bit)
─ using session charset: UTF-8
─ using options ‘--no-manual --as-cran’
✓ checking for file ‘DIAlignR/DESCRIPTION’ ...
─ checking extension type ... Package
─ this is package ‘DIAlignR’ version ‘0.99.9’
─ package encoding: UTF-8
✓ checking package namespace information ...
✓ checking package dependencies (3.6s)
✓ checking if this is a source package ...
✓ checking if there is a namespace
✓ checking for executable files (534ms)
✓ checking for hidden files and directories
✓ checking for portable file names ...
✓ checking for sufficient/correct file permissions
✓ checking serialization versions
✓ checking whether package ‘DIAlignR’ can be installed (33.6s)
N checking installed package size
installed size is 9.2Mb
sub-directories of 1Mb or more:
extdata 3.6Mb
libs 5.0Mb
✓ checking package directory ...
✓ checking for future file timestamps (571ms)
✓ checking ‘build’ directory
✓ checking DESCRIPTION meta-information ...
✓ checking top-level files
✓ checking for left-over files
✓ checking index information ...
✓ checking package subdirectories ...
✓ checking R files for non-ASCII characters ...
✓ checking R files for syntax errors ...
✓ checking whether the package can be loaded (727ms)
✓ checking whether the package can be loaded with stated dependencies (719ms)
✓ checking whether the package can be unloaded cleanly (715ms)
✓ checking whether the namespace can be loaded with stated dependencies (631ms)
✓ checking whether the namespace can be unloaded cleanly (723ms)
✓ checking loading without being on the library search path (804ms)
✓ checking dependencies in R code (2s)
✓ checking S3 generic/method consistency (1.8s)
✓ checking replacement functions (761ms)
✓ checking foreign function calls (817ms)
✓ checking R code for possible problems (5.3s)
✓ checking Rd files (388ms)
✓ checking Rd metadata ...
✓ checking Rd line widths ...
✓ checking Rd cross-references ...
✓ checking for missing documentation entries (750ms)
✓ checking for code/documentation mismatches (2.4s)
✓ checking Rd \usage sections (2.1s)
✓ checking Rd contents ...
✓ checking for unstated dependencies in examples ...
✓ checking contents of ‘data’ directory ...
✓ checking data for non-ASCII characters ...
✓ checking data for ASCII and uncompressed saves ...
✓ checking line endings in C/C++/Fortran sources/headers ...
✓ checking pragmas in C/C++ headers and code ...
✓ checking compilation flags used
✓ checking compiled code ...
✓ checking installed files from ‘inst/doc’ ...
✓ checking files in ‘vignettes’ ...
✓ checking examples (9s)
✓ checking for unstated dependencies in ‘tests’ ...
─ checking tests ...
✓ Running ‘testthat.R’ (4.7s)
✓ checking for unstated dependencies in vignettes (5s)
✓ checking package vignettes in ‘inst/doc’
✓ checking re-building of vignette outputs (7.1s)
See
‘/media/justincsing/ExtraDrive1/Documents2/Roest_Lab/Github/DIAlignR.Rcheck/00check.log’
for details.
── R CMD check results ──────────────────────────────────── DIAlignR 0.99.9 ────
Duration: 1m 24.2s
> checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
extdata 3.6Mb
libs 5.0Mb
0 errors ✓ | 0 warnings ✓ | 1 note x
R CMD check succeeded
I used the previous implemented parameter for mzPntrs to allow stored mz objects to be used. DrawAlignR passes an mzPntrs object to DIAlignR. Adjusted tests where necessary, all tests passed.