* using log directory ‘/srv/hornik/tmp/CRAN/SIPmg.Rcheck’ * using R Under development (unstable) (2023-10-25 r85412) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (15) GNU Fortran (Debian 13.2.0-4) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘SIPmg/DESCRIPTION’ ... OK * this is package ‘SIPmg’ version ‘1.5.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Pranav Sampara ’ Possibly misspelled words in DESCRIPTION: metagenomic (17:142) quantitaive (17:48) Found the following (possibly) invalid URLs: URL: https://journals.asm.org/doi/10.1128/AEM.02280-15 (moved to https://journals.asm.org/doi/10.1128/aem.02280-15) From: inst/doc/SIPmg-vignette.html Status: 301 Message: Moved Permanently URL: https://journals.asm.org/doi/10.1128/AEM.02609-06 (moved to https://journals.asm.org/doi/10.1128/aem.02609-06) From: inst/doc/SIPmg-vignette.html Status: 301 Message: Moved Permanently URL: https://journals.asm.org/doi/10.1128/mSphere.00085-21 (moved to https://journals.asm.org/doi/10.1128/msphere.00085-21) From: inst/doc/SIPmg-vignette.html Status: 301 Message: Moved Permanently URL: https://journals.asm.org/doi/10.1128/mSystems.00151-20 (moved to https://journals.asm.org/doi/10.1128/msystems.00151-20) From: inst/doc/SIPmg-vignette.html Status: 301 Message: Moved Permanently URL: https://journals.asm.org/doi/full/10.1128/AEM.02280-15 (moved to https://journals.asm.org/doi/full/10.1128/aem.02280-15) From: inst/doc/SIPmg-vignette.html Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 ‘SIPmg’ can be installed ... [16s/16s] OK * checking package directory ... OK * checking for future file timestamps ... 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [5s/5s] OK * checking whether the package can be loaded with stated dependencies ... [5s/5s] OK * checking whether the package can be unloaded cleanly ... [5s/5s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK * checking whether the namespace can be unloaded cleanly ... [5s/5s] OK * checking loading without being on the library search path ... [5s/5s] OK * checking use of S3 registration ... 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 ... [22s/22s] NOTE .qSIP_bootstrap: no visible binding for global variable ‘OTU’ calc_Mheavymax_MAGs: no visible binding for global variable ‘Gi’ calc_Mheavymax_MAGs: no visible binding for global variable ‘Mlight’ calc_Mheavymax_MAGs: no visible binding for global variable ‘df_OTU_s’ calc_atom_excess_MAGs: no visible binding for global variable ‘Mlab’ calc_atom_excess_MAGs: no visible binding for global variable ‘Mlight’ calc_atom_excess_MAGs: no visible binding for global variable ‘Mheavymax’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Buoyant_density’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Count’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘IS_CONTROL’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘OTU’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Replicate’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘W’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Wm’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Wlab’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Wlight’ qSIP_atom_excess_MAGs: no visible global function definition for ‘setNames’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘.’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Z’ qSIP_atom_excess_MAGs: no visible binding for global variable ‘Mlight’ qSIP_atom_excess_format_MAGs: no visible binding for global variable ‘Buoyant_density’ qSIP_atom_excess_format_MAGs: no visible binding for global variable ‘Count’ qSIP_bootstrap_fcr: no visible binding for global variable ‘OTU’ Undefined global functions or variables: . Buoyant_density Count Gi IS_CONTROL Mheavymax Mlab Mlight OTU Replicate W Wlab Wlight Wm Z df_OTU_s setNames Consider adding importFrom("stats", "setNames") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'calc_Mheavymax_MAGs.Rd' ‘df_OTU_s1’ Documented arguments not in \usage in Rd file 'calc_Mheavymax_MAGs.Rd': ‘Mlight’ ‘Gi’ Undocumented arguments in Rd file 'calc_atom_excess_MAGs.Rd' ‘df_OTU_s1’ Documented arguments not in \usage in Rd file 'calc_atom_excess_MAGs.Rd': ‘Mlab’ ‘Mlight’ ‘Mheavymax’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [4s/4s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [13s/13s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [63s/63s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 2 NOTEs