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shubham1637 / DIAlignR

This is a R package for alignment of DIA mass-spec data
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Feature/alignment mapping table #21

Closed singjc closed 1 year ago

singjc commented 2 years ago

Implemented option to save a map of aligned experiment features to reference features. This is for star alignment..

Local tests pass on my machine. Currently trying to build on Travis-CI...

Tests run on Graham

R CMD check

R CMD check $ R CMD build DIAlignR --no-build-vignettes && R CMD check --no-vignettes --no-build-vignettes --ignore-vignettes DIAlignR_2.3.3.tar.gz * checking for file ‘DIAlignR/DESCRIPTION’ ... OK * preparing ‘DIAlignR’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘DIAlignR/snakemake’ * looking to see if a ‘data/datalist’ file should be added * building ‘DIAlignR_2.3.3.tar.gz’ Warning in sprintf(gettext(fmt, domain = domain), ...) : one argument not used by format 'invalid uid value replaced by that for user 'nobody'' Warning: invalid uid value replaced by that for user 'nobody' Warning in sprintf(gettext(fmt, domain = domain), ...) : one argument not used by format 'invalid gid value replaced by that for user 'nobody'' Warning: invalid gid value replaced by that for user 'nobody' * using log directory ‘/home/singjust/dev/DIAlignR.Rcheck’ * using R version 4.1.2 (2021-11-01) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--ignore-vignettes’ * checking for file ‘DIAlignR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DIAlignR’ version ‘2.3.3’ * 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 ... NOTE Found the following hidden files and directories: .dockerignore These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DIAlignR’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.9Mb sub-directories of 1Mb or more: extdata 4.1Mb metabo 4.2Mb ptms 1.5Mb * 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 R 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘magrittr’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE alignTargetedRuns: no visible binding for global variable ‘peptide_id’ alignTargetedRuns : : no visible global function definition for ‘.’ alignTargetedRuns: no visible binding for global variable ‘intensity’ alignToRoot4: no visible binding for global variable ‘trees’ alignToRoot4: no visible binding for global variable ‘precursors’ alignToRoot4: no visible binding for global variable ‘intensity’ childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf, x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x))) distMat.rSqrd : : : no visible binding for global variable ‘RT.ref’ distMat.rSqrd : : : no visible binding for global variable ‘RT.eXp’ fetchPrecursorsInfo: no visible binding for global variable ‘transition_id’ fetchPrecursorsInfo: no visible global function definition for ‘.’ fetchPrecursorsInfo: no visible binding for global variable ‘transition_group_id’ fetchTransitionsFromRun: no visible binding for global variable ‘intensity’ fetchTransitionsFromRun: no visible global function definition for ‘.’ fetchTransitionsFromRun: no visible binding for global variable ‘transition_group_id’ fetchTransitionsFromRun: no visible binding for global variable ‘peak_group_rank’ fetchTransitionsFromRun: no visible global function definition for ‘head’ getNativeIDs: no visible binding for global variable ‘peptide_id’ getPeptideScores: no visible binding for global variable ‘col2’ getPeptideScores: no visible binding for global variable ‘run’ getQuery: no visible binding for global variable ‘identifying.transitionPEPfilter’ getRTdf: no visible binding for global variable ‘peak_group_rank’ getRTdf: no visible binding for global variable ‘m_score’ getRTdf: no visible global function definition for ‘.’ getRTdf: no visible binding for global variable ‘transition_group_id’ getRTdf: no visible binding for global variable ‘RT’ getRefRun : : no visible binding for global variable ‘pvalue’ ipfReassignFDR: no visible binding for global variable ‘ref_run’ ipfReassignFDR: no visible binding for global variable ‘run’ ipfReassignFDR: no visible global function definition for ‘.’ ipfReassignFDR: no visible binding for global variable ‘i.to’ ipfReassignFDR: no visible binding for global variable ‘m_score_new’ ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’ ipfReassignFDR: no visible binding for global variable ‘m_score’ mstAlignRuns: no visible binding for global variable ‘ropenms’ mstAlignRuns: no visible binding for global variable ‘peptide_id’ mstAlignRuns : : no visible global function definition for ‘.’ mstAlignRuns: no visible binding for global variable ‘intensity’ mstScript1: no visible binding for global variable ‘ropenms’ mstScript2: no visible binding for global variable ‘fileInfo’ mstScript2: no visible binding for global variable ‘peptide_id’ mstScript2: no visible binding for global variable ‘features’ mstScript2 : : no visible global function definition for ‘.’ mstScript2 : : no visible binding for global variable ‘features’ mstScript2: no visible binding for global variable ‘intensity’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘run’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘transition_group_id’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘feature_id’ progAlignRuns: no visible binding for global variable ‘peptide_id’ progAlignRuns : : no visible global function definition for ‘.’ progAlignRuns: no visible binding for global variable ‘intensity’ progComb3: no visible binding for global variable ‘precursors’ progComb3: no visible binding for global variable ‘ropenms’ progSplit2: no visible binding for global variable ‘trees’ progSplit2: no visible binding for global variable ‘scoreFile’ progSplit2: no visible binding for global variable ‘precursors’ progSplit2 : : no visible global function definition for ‘.’ progSplit2: no visible binding for global variable ‘ropenms’ progSplit4: no visible binding for global variable ‘precursors’ progSplit4 : : no visible global function definition for ‘.’ progSplit4: no visible binding for global variable ‘intensity’ progTree1: no visible binding for global variable ‘ropenms’ progTree1: no visible binding for global variable ‘peptide_id’ reIntensity: no visible binding for global variable ‘run’ reIntensity: no visible binding for global variable ‘alignment_rank’ recalculateIntensity: no visible binding for global variable ‘peptide_id’ recalculateIntensity: no visible binding for global variable ‘chromatogramIndex’ script2: no visible binding for global variable ‘fileInfo’ script2: no visible binding for global variable ‘peptide_id’ script2 : : no visible global function definition for ‘.’ script2: no visible binding for global variable ‘features’ script2: no visible binding for global variable ‘globalFits’ script2: no visible binding for global variable ‘RSE’ script2: no visible binding for global variable ‘intensity’ setRootRank : : no visible global function definition for ‘.’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘reference_feature_id’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘experiment_feature_id’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘ALIGNMENT_GROUP_ID’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘REFERENCE’ writeOutFeatureAlignmentMap: no visible global function definition for ‘.’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘i.to’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘outFile’ writeTables: no visible binding for global variable ‘peptide_id’ writeTables: no visible binding for global variable ‘run’ writeTables: no visible binding for global variable ‘precursor’ Undefined global functions or variables: . ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank chromatogramIndex col2 experiment_feature_id feature_id features fileInfo globalFits head i.to identifying.transitionPEPfilter intensity m_score m_score_new ms2_m_score outFile peak_group_rank peptide_id precursor precursors pvalue ref_run reference_feature_id ropenms run scoreFile transition_group_id transition_id trees Consider adding importFrom("datasets", "trees") importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'alignTargetedRuns': alignTargetedRuns Code: function(dataPath, outFile = "DIAlignR", params = paramsDIAlignR(), oswMerged = TRUE, scoreFile = NULL, runs = NULL, peps = NULL, refRun = NULL, applyFun = lapply, saveAlignmentMap = FALSE) Docs: function(dataPath, outFile = "DIAlignR", params = paramsDIAlignR(), oswMerged = TRUE, scoreFile = NULL, runs = NULL, peps = NULL, refRun = NULL, applyFun = lapply) Argument names in code not in docs: saveAlignmentMap Codoc mismatches from documentation object 'alignToRef': alignToRef Code: function(eXp, ref, refIdx, fileInfo, XICs, XICs.ref, params, df, globalFits, RSE, feature_alignment_map = NULL) Docs: function(eXp, ref, refIdx, fileInfo, XICs, XICs.ref, params, df, globalFits, RSE) Argument names in code not in docs: feature_alignment_map Codoc mismatches from documentation object 'perBatch': perBatch Code: function(iBatch, peptides, multipeptide, refRuns, precursors, prec2chromIndex, fileInfo, mzPntrs, params, globalFits, RSE, applyFun = lapply, multiFeatureAlignmentMap = NULL) Docs: function(iBatch, peptides, multipeptide, refRuns, precursors, prec2chromIndex, fileInfo, mzPntrs, params, globalFits, RSE, applyFun = lapply) Argument names in code not in docs: multiFeatureAlignmentMap * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/singjust/dev/DIAlignR.Rcheck/00check.log’ for details.

BiocCheck

BiocCheck > BiocCheck::BiocCheck("./DIAlignR") This is BiocCheck version 1.30.0. BiocCheck is a work in progress. Output and severity of issues may change. Installing package... * Checking Package Dependencies... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 85 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). function (object) alignTargetedRuns (peptide_id) alignTargetedRuns (.) alignTargetedRuns (intensity) alignToRoot4 (trees) alignToRoot4 (precursors) alignToRoot4 (intensity) distMat.rSqrd (RT.ref) distMat.rSqrd (RT.eXp) fetchPrecursorsInfo (transition_id) fetchPrecursorsInfo (.) fetchPrecursorsInfo (transition_group_id) fetchTransitionsFromRun (intensity) fetchTransitionsFromRun (.) fetchTransitionsFromRun (transition_group_id) fetchTransitionsFromRun (peak_group_rank) fetchTransitionsFromRun (head) getNativeIDs (peptide_id) getPeptideScores (col2) getPeptideScores (run) getQuery (identifying.transitionPEPfilter) getRefRun (pvalue) getRTdf (peak_group_rank) getRTdf (m_score) getRTdf (.) getRTdf (transition_group_id) getRTdf (RT) ipfReassignFDR (ref_run) ipfReassignFDR (run) ipfReassignFDR (.) ipfReassignFDR (i.to) ipfReassignFDR (m_score_new) ipfReassignFDR (ms2_m_score) ipfReassignFDR (m_score) mstAlignRuns (ropenms) mstAlignRuns (peptide_id) mstAlignRuns (.) mstAlignRuns (intensity) mstScript1 (ropenms) mstScript2 (fileInfo) mstScript2 (peptide_id) mstScript2 (features) mstScript2 (.) mstScript2 (features) mstScript2 (intensity) populateReferenceExperimentFeatureAlignmentMap (run) populateReferenceExperimentFeatureAlignmentMap (transition_group_id) populateReferenceExperimentFeatureAlignmentMap (feature_id) progAlignRuns (peptide_id) progAlignRuns (.) progAlignRuns (intensity) progComb3 (precursors) progComb3 (ropenms) progSplit2 (trees) progSplit2 (scoreFile) progSplit2 (precursors) progSplit2 (.) progSplit2 (ropenms) progSplit4 (precursors) progSplit4 (.) progSplit4 (intensity) progTree1 (ropenms) progTree1 (peptide_id) recalculateIntensity (peptide_id) recalculateIntensity (chromatogramIndex) reIntensity (run) reIntensity (alignment_rank) script2 (fileInfo) script2 (peptide_id) script2 (.) script2 (features) script2 (globalFits) script2 (RSE) script2 (intensity) setRootRank (.) traverseUp (temp) writeOutFeatureAlignmentMap (reference_feature_id) writeOutFeatureAlignmentMap (experiment_feature_id) writeOutFeatureAlignmentMap (ALIGNMENT_GROUP_ID) writeOutFeatureAlignmentMap (REFERENCE) writeOutFeatureAlignmentMap (.) writeOutFeatureAlignmentMap (i.to) writeOutFeatureAlignmentMap (outFile) writeTables (peptide_id) writeTables (run) writeTables (precursor) * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking version number validity... * WARNING: y of x.y.z version should be even in release * Checking R Version dependency... * NOTE: Update R version dependency from 4.0 to 4.1.0. * Checking package size... Skipped... only checked on source tarball * Checking individual file sizes... * WARNING: The following files are over 5MB in size: '.git/objects/pack/pack-1b9a369c28b4aa846366eb25d211ad2c6edecf78.pack' * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * NOTE: Consider adding these automatically suggested biocViews: Coverage See http://bioconductor.org/developers/how-to/biocViews/ * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking License: for restrictive use... * Checking DESCRIPTION/NAMESPACE consistency... * WARNING: Import magrittr in NAMESPACE as well as DESCRIPTION. * Checking .Rbuildignore... * Checking vignette directory... * NOTE: Potential intermediate files found: vignettes/dialignr-vignette.html * Checking package installation calls in R code... * Checking for library/require of DIAlignR... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() Found in files: R/align_dia_runs.R (line 179, column 28) R/get_peaks_chromatograms.R (line 69, column 15) R/get_peaks_chromatograms.R (line 70, column 14) R/merge_chromatogram.R (line 43, column 23) R/merge_runs.R (line 244, column 9) R/merge_runs.R (line 246, column 12) R/merge_runs.R (line 261, column 12) R/merge_runs.R (line 312, column 10) R/merge_runs.R (line 316, column 10) R/merge_runs.R (line 320, column 10) R/merge_runs.R (line 464, column 25) R/merge_runs.R (line 465, column 17) R/merge_runs.R (line 492, column 29) R/merge_runs.R (line 493, column 15) R/mstAlign.R (line 256, column 28) R/post_alignment.R (line 177, column 12) R/post_alignment.R (line 191, column 12) R/post_alignment.R (line 223, column 18) R/progressive_alignment.R (line 163, column 28) R/progressive_alignment.R (line 533, column 28) R/progressive_alignment.R (line 598, column 28) R/pyopenms.R (line 126, column 21) R/scripts.R (line 184, column 28) R/scripts.R (line 420, column 28) R/utils.R (line 733, column 3) R/utils.R (line 807, column 7) R/utils.R (line 829, column 13) R/utils.R (line 843, column 14) R/utils.R (line 867, column 8) * NOTE: Avoid 1:...; use seq_len() or seq_along() Found in files: align_dia_runs.R (line 161, column 12) get_filenames.R (line 189, column 25) get_global_fit.R (line 256, column 33) merge_chromatogram.R (line 115, column 41) merge_chromatogram.R (line 115, column 74) merge_order.R (line 22, column 7) merge_order.R (line 107, column 16) merge_order.R (line 123, column 21) merge_order.R (line 202, column 21) merge_order.R (line 317, column 19) merge_order.R (line 418, column 20) merge_order.R (line 503, column 12) merge_osw_mzml.R (line 79, column 12) merge_runs.R (line 135, column 16) merge_runs.R (line 146, column 32) merge_runs.R (line 261, column 19) merge_runs.R (line 386, column 18) mstAlign.R (line 213, column 19) mstAlign.R (line 215, column 24) mstAlign.R (line 220, column 18) mstAlign.R (line 238, column 12) mstAlign.R (line 340, column 14) pairwise_pep_peak_corp.R (line 355, column 20) pairwise_pep_peak_corp.R (line 355, column 42) pairwise_pep_peak_corp.R (line 365, column 20) pairwise_pep_peak_corp.R (line 365, column 42) post_alignment.R (line 105, column 20) post_alignment.R (line 105, column 42) progressive_alignment.R (line 489, column 21) progressive_alignment.R (line 650, column 12) read_osw.R (line 102, column 12) read_osw.R (line 373, column 24) read_osw.R (line 645, column 27) scripts.R (line 166, column 12) scripts.R (line 377, column 19) scripts.R (line 379, column 24) scripts.R (line 384, column 18) scripts.R (line 402, column 12) utils.R (line 432, column 34) utils.R (line 756, column 31) utils.R (line 758, column 27) utils.R (line 789, column 32) utils.R (line 800, column 127) utils.R (line 801, column 144) visualise_chromatograms.R (line 32, column 40) visualise_chromatograms.R (line 177, column 20) visualise_chromatograms.R (line 177, column 42) * NOTE: Avoid the use of 'paste' in condition signals Found in files: R/align_dia_runs.R (line 192, column 11) R/align_dia_runs.R (line 265, column 13) R/align_dia_runs.R (line 554, column 55) R/align_dia_runs.R (line 562, column 54) R/align_dia_runs.R (line 570, column 63) R/get_global_fit.R (line 60, column 29) R/get_peaks_chromatograms.R (line 194, column 26) R/merge_runs.R (line 467, column 57) R/mstAlign.R (line 260, column 11) R/mstAlign.R (line 422, column 55) R/mstAlign.R (line 430, column 66) R/mstAlign.R (line 438, column 63) R/progressive_alignment.R (line 167, column 11) R/progressive_alignment.R (line 537, column 11) R/progressive_alignment.R (line 602, column 11) R/read_osw.R (line 380, column 15) R/read_osw.R (line 383, column 15) R/read_osw.R (line 651, column 13) R/scripts.R (line 188, column 11) R/scripts.R (line 424, column 11) * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions Found in files: R/align_dia_runs.R (line 562, column 22) R/align_dia_runs.R (line 570, column 22) R/get_global_fit.R (line 56, column 29) R/get_global_fit.R (line 60, column 36) R/mstAlign.R (line 430, column 34) R/mstAlign.R (line 438, column 22) R/read_mzml.R (line 26, column 28) R/read_mzml.R (line 88, column 42) * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 1 times) T in R/utils.R (line 710, column 39) * WARNING: Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes Found in files: align_dia_runs.R (line 167, column 18) align_dia_runs.R (line 168, column 18) align_dia_runs.R (line 301, column 18) align_dia_runs.R (line 302, column 18) get_peaks_chromatograms.R (line 115, column 26) get_peaks_chromatograms.R (line 116, column 26) get_peaks_chromatograms.R (line 203, column 18) get_peaks_chromatograms.R (line 204, column 18) merge_osw_mzml.R (line 193, column 18) merge_osw_mzml.R (line 194, column 18) merge_osw_mzml.R (line 241, column 18) merge_osw_mzml.R (line 242, column 18) mstAlign.R (line 244, column 18) mstAlign.R (line 245, column 18) peak_area.R (line 157, column 18) peak_area.R (line 158, column 18) progressive_alignment.R (line 155, column 29) progressive_alignment.R (line 353, column 29) progressive_alignment.R (line 436, column 29) progressive_alignment.R (line 522, column 29) progressive_alignment.R (line 590, column 29) scripts.R (line 172, column 18) scripts.R (line 173, column 18) scripts.R (line 408, column 18) scripts.R (line 409, column 18) * Checking parsed R code in R directory, examples, vignettes... Found @ in man/alignedXIC.Rd Found @ in man/childXIC.Rd Found @ in man/childXICs.Rd * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) suppressWarnings() in R/chromatogram_manip.R (line 55, column 12) * Checking function lengths................................................................................................................................................... * NOTE: Recommended function length <= 50 lines. There are 29 functions > 50 lines. The longest 5 functions are: alignTargetedRuns() (R/align_dia_runs.R, line 35): 165 lines mstAlignRuns() (R/mstAlign.R, line 106): 160 lines getQuery() (R/get_osw_query.R, line 17): 158 lines mstScript2() (R/scripts.R, line 282): 148 lines getNodeRun() (R/merge_runs.R, line 56): 147 lines * Checking man page documentation... * WARNING: Add non-empty \value sections to the following man pages: man/alignToRoot4.Rd, man/mstScript1.Rd, man/mstScript2.Rd, man/progComb3.Rd, man/progSplit2.Rd, man/progSplit4.Rd, man/progTree1.Rd, man/script1.Rd, man/script2.Rd * NOTE: Consider adding runnable examples to the following man pages which document exported objects: alignToRoot4.Rd, get_ropenms.Rd, progComb3.Rd, progSplit2.Rd, progSplit4.Rd, progTree1.Rd * NOTE: Usage of dontrun{} / donttest{} found in man page examples. 5% of man pages use one of these cases. Found in the following files: createMZML.Rd createSqMass.Rd get_ropenms.Rd mstAlignRuns.Rd progAlignRuns.Rd smoothSingleXIC.Rd trimXICs.Rd * NOTE: Use donttest{} instead of dontrun{}. Found in the following files: createMZML.Rd createSqMass.Rd get_ropenms.Rd mstAlignRuns.Rd progAlignRuns.Rd smoothSingleXIC.Rd trimXICs.Rd * Checking package NEWS... * Checking unit tests... * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 2402 lines (14%) are > 80 characters long. First 6 lines: R/affine_aligned_obj.R:7 #' indexA_aligned and indexB_aligned are align... R/affine_aligned_obj.R:19 representatio... R/affine_aligned_obj.R:36 mapply(function(slotname) slot(x, slotname)... R/affine_aligned_obj.R:42 #' An S4 object for class AffineAlignObjMediu... R/affine_aligned_obj.R:45 #' path matrix is a binary matrix with ones i... R/affine_aligned_obj.R:46 #' GapOpen and GapExten are gap-opening and g... * NOTE: Consider 4 spaces instead of tabs; 11 lines (0%) contain tabs. First 6 lines: R/get_osw_query.R:288 SELECT ID, MODIFIED_SEQUENCE R/get_osw_query.R:289 FROM PEPTIDE R/get_osw_query.R:290 WHERE PEPTIDE.DECOY = 0 R/get_osw_query.R:291 ) AS PEPTIDE ON PEPTIDE_PROTEIN_MAPPING.... R/get_osw_query.R:294 SELECT ID, CHARGE, GROUP_LABEL R/get_osw_query.R:295 FROM PRECURSOR * NOTE: Consider multiples of 4 spaces for line indents, 3795 lines(22%) are not. First 6 lines: R/affine_aligned_obj.R:20 ... R/affine_aligned_obj.R:36 mapply(function(slotname) slot(x, slotname)... R/affine_aligned_obj.R:76 mapply(function(slotname) slot(x, slotname)... R/affine_aligned_obj.R:77 }) R/affine_aligned_obj.R:101 representation(s ... R/affine_aligned_obj.R:102 Tr... See http://bioconductor.org/developers/how-to/coding-style/ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... * Checking for bioc-devel mailing list subscription... * NOTE: Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel * Checking for support site registration... Maintainer is registered at support site. Package name is in support site watched tags. Summary: ERROR count: 0 WARNING count: 6 NOTE count: 18 For detailed information about these checks, see the BiocCheck vignette, available at https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output $error character(0) $warning [1] "y of x.y.z version should be even in release" [2] "The following files are over 5MB in size: '.git/objects/pack/pack-1b9a369c28b4aa846366eb25d211ad2c6edecf78.pack'" [3] "Import magrittr in NAMESPACE as well as DESCRIPTION." [4] " Avoid T/F variables; If logical, use TRUE/FALSE (found 1 times)" [5] " Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes" [6] "Add non-empty \\value sections to the following man pages: man/alignToRoot4.Rd, man/mstScript1.Rd, man/mstScript2.Rd, man/progComb3.Rd, man/progSplit2.Rd, man/progSplit4.Rd, man/progTree1.Rd, man/script1.Rd, man/script2.Rd" $note [1] "Consider clarifying how 85 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within()." [2] "Update R version dependency from 4.0 to 4.1.0." [3] "Consider adding these automatically suggested biocViews: Coverage" [4] "Potential intermediate files found:" [5] " Avoid sapply(); use vapply()" [6] " Avoid 1:...; use seq_len() or seq_along()" [7] " Avoid the use of 'paste' in condition signals" [8] " Avoid redundant 'stop' and 'warn*' in signal conditions" [9] "Use accessors; don't access S4 class slots via '@' in examples/vignettes." [10] "Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)" [11] "Recommended function length <= 50 lines." [12] "Consider adding runnable examples to the following man pages which document exported objects:" [13] "Usage of dontrun{} / donttest{} found in man page examples." [14] "Use donttest{} instead of dontrun{}." [15] "Consider shorter lines; 2402 lines (14%) are > 80 characters long." [16] "Consider 4 spaces instead of tabs; 11 lines (0%) contain tabs." [17] "Consider multiples of 4 spaces for line indents, 3795 lines(22%) are not." [18] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials). Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"