* using log directory ‘/srv/hornik/tmp/CRAN/protti.Rcheck’ * using R Under development (unstable) (2024-01-29 r85841) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (3) Debian flang-new version 17.0.6 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘protti/DESCRIPTION’ ... OK * this is package ‘protti’ version ‘0.7.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [6s/11s] NOTE Maintainer: ‘Jan-Philipp Quast ’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid URLs: URL: https://3dmol.csb.pitt.edu/index.html From: inst/doc/protein_structure_workflow.html Status: Error Message: server certificate verification failed. CAfile: none CRLfile: none (Status without verification: OK) * 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 ‘protti’ can be installed ... [8s/9s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘revdep’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] 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 ... [13s/13s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) assign_missingness.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) assign_missingness.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) assign_missingness.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) assign_missingness.Rd:63-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculate_diff_abundance.Rd:105-107: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculate_diff_abundance.Rd:108-115: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculate_diff_abundance.Rd:116-126: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculate_diff_abundance.Rd:127-131: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) diff_abundance.Rd:15-17: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) diff_abundance.Rd:18-25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) diff_abundance.Rd:26-36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) diff_abundance.Rd:37-41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extract_metal_binders.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_aligned_error.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_aligned_error.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_aligned_error.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_aligned_error.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_alphafold_prediction.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:85-89: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:90-92: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:93-95: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:96-98: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_metal_pdb.Rd:99-101: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:25-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:31-35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:36-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:39-41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb.Rd:46-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:24-26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:27-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:38-42: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:51-53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fetch_pdb_structure.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:51-53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:64-67: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:68-71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:72-73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) find_peptide_in_structure.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fit_drc_4p.Rd:86: Lost braces 86 | (measured points). If \ code{include_models = TURE}, a list is returned that contains: | ^ checkRd: (-1) fit_drc_4p.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) fit_drc_4p.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict_alphafold_domain.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict_alphafold_domain.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict_alphafold_domain.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] 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 ... [19s/19s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [14s/14s] OK Running ‘testthat.R’ [14s/14s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [5s/5s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 NOTEs