check for unique function names

[mpadge]

Using [new pkgstats::pkgstats_fn_names() function, and the database from applying that to all of CRAN (as pkgstats-fn-names.Rds). All function names can then be compared with entries from that database, and any duplicated names dumped into report, identifying packages which already claim those names. Ping @maelle

[mpadge]

Closing with this demo result, which appears in the summary with details in Other Checks:

---

Checks for lme4 (v1.1-27)

git hash: 6a6d121c

• ✔️ Package is already on CRAN.
• ✖️ does not have a 'codemeta.json' file.
• ✖️ does not have a 'contributing' file.
• ✖️ does not use 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [checkConv, devcomp, glmerLaplaceHandle, glmFamily, isSingular, lme4_testlevel, lme4-package, lmResp, merPredD, mkMerMod, mkRespMod, mkSimulateTemplate, mkVarCorr, nlformula, pvalues, refitML, rePos, residuals.merMod, simulate.formula, troubleshooting].
• ✖️ Function names are duplicated in other packages
• ✖️ Package uses global assignment operator ('<<-').
• ✔️ Package has continuous integration checks.
• ✖️ Package coverage failed
• ✖️ R CMD check process failed with message: 'object 'cmdargs' not found'.

Important: All failing checks above must be addressed prior to proceeding

Package License: GPL (>=2)

---

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	2678
internal	lme4	1035
internal	stats	341
internal	methods	105
depends	Matrix	13
imports	utils	48
imports	nlme	27
imports	lattice	17
imports	graphics	16
imports	parallel	6
imports	splines	5
imports	MASS	5
imports	boot	3
imports	minqa	2
imports	grid	1
imports	nloptr	1
imports	statmod	1
suggests	ggplot2	2
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	PKPDmodels	NA
suggests	MEMSS	NA
suggests	testthat	NA
suggests	mlmRev	NA
suggests	optimx	NA
suggests	gamm4	NA
suggests	pbkrtest	NA
suggests	HSAUR3	NA
suggests	numDeriv	NA
suggests	car	NA
suggests	dfoptim	NA
suggests	mgcv	NA
linking_to	Rcpp	NA
linking_to	RcppEigen	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

list (410), if (206), c (194), lapply (97), is.null (92), attr (75), nrow (70), for (67), substitute (56), vapply (51), do.call (43), eval (43), seq_along (43), data.frame (38), t (29), drop (26), ncol (25), numeric (25), levels (24), sqrt (24), as.numeric (23), match.call (23), seq_len (23), diag (21), which (21), stopifnot (19), any (18), matrix (18), parent.frame (18), unlist (18), environment (17), list2env (17), sapply (17), colnames (16), rep.int (16), tryCatch (16), unname (16), call (15), is.na (15), rep (15), class (14), rbind (14), structure (13), inherits (12), sum (12), as.integer (11), deparse (11), dim (11), missing (11), paste (11), seq (11), setdiff (11), unique (11), UseMethod (11), all (10), beta (10), cbind (10), formals (10), max (10), abs (9), apply (9), as.data.frame (9), as.list (9), grep (9), array (8), diff (8), factor (8), get (8), is.numeric (8), log (8), norm (8), all.vars (7), as.name (7), getOption (7), match (7), nlevels (7), order (7), range (7), rownames (7), split (7), as.logical (6), as.vector (6), dimnames (6), gl (6), solve (6), chol (5), cumsum (5), lower.tri (5), new.env (5), scale (5), as.matrix (4), bquote (4), expand.grid (4), format (4), ifelse (4), is.character (4), labels (4), local (4), logical (4), Map (4), mapply (4), nchar (4), outer (4), row.names (4), sprintf (4), subset (4), switch (4), vector (4), warning (4), with (4), character (3), col (3), eval.parent (3), gamma (3), integer (3), is.matrix (3), mode (3), nzchar (3), quote (3), rev (3), round (3), substring (3), summary (3), Sys.getenv (3), tapply (3), tcrossprod (3), warnings (3), as.call (2), as.double (2), as.environment (2), crossprod (2), debug (2), eigen (2), emptyenv (2), exp (2), expression (2), getNamespaceExports (2), getRversion (2), gettextf (2), identical (2), identity (2), intersect (2), is.finite (2), is.list (2), ordered (2), parent.env (2), pmax (2), pmin (2), qr (2), Reduce (2), replicate (2), return (2), row (2), rowSums (2), stderr (2), sub (2), suppressMessages (2), suppressWarnings (2), sys.frame (2), system.time (2), table (2), union (2), withCallingHandlers (2), abbreviate (1), alist (1), as.expression (1), asNamespace (1), assign (1), attributes (1), by (1), cat (1), conditionCall (1), conditionMessage (1), force (1), grepl (1), gsub (1), I (1), is.data.frame (1), is.factor (1), is.logical (1), match.arg (1), mean (1), min (1), ngettext (1), parse (1), pi (1), pmatch (1), print (1), qr.coef (1), qr.X (1), Recall (1), sign (1), slice.index (1), sort (1), standardGeneric (1), stop (1), strsplit (1), svd (1), sys.frames (1), sys.function (1), system (1), try (1), upper.tri (1), which.max (1), zapsmall (1)

lme4

length (172), names (77), getME (34), sigma (29), zeta (27), ff (24), devfun (23), f (20), ss (16), paste0 (14), devcomp (12), findbars (11), lengths (11), isLMM (9), condVar (7), isGLMM (7), optwrap (7), RHSForm (7), deparse1 (6), dropOffset (6), gradient (6), mkGlmerDevfun (6), mkReTrms (6), nobars_ (6), spos (6), afun (5), factory (5), getConv (5), methTitle (5), mkdevfun (5), mlist2vec (5), ngrps (5), predy (5), reexpr (5), refit (5), vec2mlist (5), vv (5), checkCtrlLevels (4), factorize (4), fillmat (4), get.orig.levs (4), GHrule (4), grpfact (4), panel.thpr (4), subbars (4), wmsg (4), anyNA (3), arrange.condVar (3), asDf0 (3), barnames (3), checkConv (3), checkFormulaData (3), checkNlevels (3), checkScaleX (3), checkZdims (3), checkZrank (3), chkRank.drop.cols (3), Cv_to_Sv (3), devCrit (3), fe.zeta (3), forceCopy (3), gaussian_simfun (3), isNLMM (3), isREML (3), levelfun (3), llikAIC (3), lmer (3), mkLmerDevfun (3), mkNewReTrms (3), mkpar (3), mkPfun (3), mmList (3), namedList (3), nlformula (3), reOnly (3), abbrDeparse (2), allvarex (2), allVarsRec (2), bdiag_to_array (2), bdiag_to_mlist (2), binomial_simfun (2), bootMer (2), calc.vcov.hess (2), chck1 (2), checkHess (2), cont (2), cov2sdcor (2), Cv_to_Vv (2), dens (2), deriv12 (2), devfun2 (2), doCheck (2), expandDoubleVerts (2), famlink (2), fitfun (2), Gamma_simfun (2), get_re (2), getInds (2), getMsg (2), getNBdisp (2), getOptfun (2), getStart (2), glFormula (2), glmer (2), glmerPwrssUpdate (2), hasNoScale (2), hasScale (2), hessian (2), inverse.gaussian_simfun (2), lFormula (2), lme4_testlevel (2), logProf (2), ltsize (2), makeFac (2), makeInteraction (2), mkBlist (2), mkDataTemplate (2), mkParsTemplate (2), mkRespMod (2), mkVarCorr (2), modelFormula (2), mypred (2), NBfun (2), negative.binomial_simfun (2), Nelder_Mead (2), nextpar (2), nextstart (2), nlmerControl (2), nlminbwrap (2), nmkbw (2), nobars (2), nobs.merMod (2), optimizeGlmer (2), optTheta (2), panel.ci (2), poisson_simfun (2), pooledSD (2), prepanel.ci (2), print.merMod (2), profnames (2), refitML (2), refitNB (2), RglmerWrkIter (2), safe_chol (2), sdiag (2), Sv_to_Cv (2), tnames (2), Vv_to_Cv (2), ad (1), all0 (1), allFit (1), anovaLmer (1), anyBars (1), array_to_bdiag (1), as.data.frame.bootMer (1), as.data.frame.ranef.mer (1), as.data.frame.thpr (1), as.data.frame.VarCorr.merMod (1), as.function.merMod (1), attr_fun (1), augment.RE (1), bootFun (1), cat.f (1), cfun (1), check.boundary (1), checkArgs (1), checkResponse (1), chk.cconv (1), chk.convOpt (1), chooseFace (1), coef.lmList4 (1), coefMer (1), colSort (1), combineLists (1), confint.bootMer (1), confint.lmList4 (1), confint.merMod (1), confint.thpr (1), cooks.distance.influence.merMod (1), cooks.distance.merMod (1), deleteGroup (1), densityplot.thpr (1), deviance.merMod (1), df.residual.merMod (1), dfbeta.influence.merMod (1), dfbetas.influence.merMod (1), dim.merMod (1), dotplot.coef.mer (1), dotplot.ranef.mer (1), dp (1), drop1.merMod (1), dummy (1), est_theta (1), expandDoubleVert (1), expandSlash (1), extractAIC.merMod (1), family.glmResp (1), family.lmResp (1), family.merMod (1), family.nlsResp (1), family2char (1), fb (1), fitted.merMod (1), fixed.effects (1), fixef.merMod (1), format.perc (1), formatVC (1), formula.lmList4 (1), formula.merMod (1), frecurse (1), gamma.shape.merMod (1), get_clen (1), get.which (1), getCovariateFormula (1), getData.merMod (1), getFixedFormula (1), getGroups.lmList4 (1), getGroupsFormula (1), getGroupsFormula.merMod (1), getIDLabels (1), getME.merMod (1), getNBdisp.fam (1), glmer.nb (1), glmerLaplaceHandle (1), GQdk (1), grad.ctr (1), grad.ctr2 (1), grad.ctr3 (1), grad.ctr4 (1), hatvalues.merMod (1), influence.merMod (1), isAnyArgBar (1), isBar (1), isFlexLambda (1), isGLMlist (1), isGLMM.merMod (1), isLMM.merMod (1), isNBfamily (1), isNested (1), isNLMM.merMod (1), isRE (1), isREML.merMod (1), isSingular (1), lmList (1), log.thpr (1), logLik.merMod (1), lp (1), makeOp (1), matchNames (1), mcmcsamp (1), mcmcsamp.merMod (1), mkMerMod (1), mkMinimalData (1), mkOptCtrl (1), mlist_to_array (1), mmList.formula (1), mmList.merMod (1), model.frame.merMod (1), nafun (1), ngrps.default (1), ngrps.factor (1), ngrps.merMod (1), nlmer (1), noLHSform (1), normalizeFamilyName (1), npar.merMod (1), optimizeLmer (1), panel.blank (1), panelfun (1), plot.allFit (1), plot.coef.mer (1), plot.lmList4.confint (1), plot.ranef.mer (1), predict.merMod (1), print.allFit (1), print.bootMer (1), print.bootWarnings (1), print.ranef.mer (1), print.summary.merMod (1), print.VarCorr.merMod (1), profile.merMod (1), qqmath.ranef.mer (1), quickSimulate (1), random.effects (1), ranef.merMod (1), refit.merMod (1), refit2.merMod (1), refitML.merMod (1), reFormHack (1), REMLcrit (1), rep_len (1), rePCA (1), rePCA.merMod (1), residuals.glmResp (1), residuals.lmResp (1), sdcor2cov (1), simulate.formula_lhs_ (1), slashTerms (1), splitFormula (1), svals (1), tmpf (1), Tpfun (1), VarCorr.merMod (1), varex (1), vfun (1)

stats

formula (81), start (23), model.frame (21), logLik (16), fitted (14), predict (13), setNames (12), BIC (10), model.matrix (10), na.action (9), vcov (9), sd (7), var (7), gaussian (6), nobs (6), residuals (6), model.response (5), getCall (4), hat (4), hatvalues (4), na.omit (4), update (4), as.formula (3), coef (3), contrasts (3), df (3), model.offset (3), na.exclude (3), ave (2), binomial (2), coefficients (2), density (2), deviance (2), model.extract (2), model.weights (2), profile (2), qnorm (2), rbinom (2), resid (2), rnorm (2), step (2), asOneSidedFormula (1), confint (1), D (1), delete.response (1), df.residual (1), dfbeta (1), effects (1), end (1), Gamma (1), glm (1), inverse.gaussian (1), na.pass (1), nlminb (1), optim (1), optimize (1), pchisq (1), pf (1), poisson (1), qchisq (1), qt (1), quantile (1), simulate (1)

methods

el (20), is (15), initialize (12), new (12), setRefClass (10), setClass (9), as (7), extends (3), representation (3), setGeneric (3), setMethod (3), slotNames (3), rbind2 (2), getClass (1), getDataPart (1), slot (1)

utils

data (43), stack (2), head (1), methods (1), str (1)

nlme

fixef (17), ranef (6), VarCorr (4)

lattice

trellis.par.get (8), strip.custom (3), current.panel.limits (2), qqmath (2), llines (1), panel.number (1)

graphics

frame (13), abline (1), text (1), title (1)

Matrix

drop0 (4), rankMatrix (4), as.matrix (1), bdiag (1), Diagonal (1), fac2sparse (1), sparseMatrix (1)

parallel

clusterExport (2), mclapply (2), makeCluster (1), parLapply (1)

MASS

negative.binomial (5)

splines

interpSpline (4), backSpline (1)

boot

boot.ci (3)

ggplot2

facet_wrap (1), theme (1)

minqa

bobyqa (2)

grid

gpar (1)

nloptr

nloptr (1)

statmod

rinvgauss (1)

---

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in C++ (23% in 6 files) and R (77% in 25 files)
• 4 authors
• 1 vignette
• 11 internal data files
• 12 imported packages
• 154 exported functions (median 13 lines of code)
• 606 non-exported functions in R (median 8 lines of code)
• 254 R functions (median 5 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	25	86.3
files_src	6	90.2
files_vignettes	7	98.5
files_tests	82	99.7
loc_R	7628	97.7	TRUE
loc_src	2244	77.8
loc_vignettes	3593	99.1	TRUE
loc_tests	5394	98.4	TRUE
num_vignettes	1	64.8
data_size_total	153096	85.6
data_size_median	733	62.4
n_fns_r	760	98.8	TRUE
n_fns_r_exported	154	97.7	TRUE
n_fns_r_not_exported	606	98.9	TRUE
n_fns_src	254	91.1
n_fns_per_file_r	16	93.5
n_fns_per_file_src	30	97.0	TRUE
num_params_per_fn	3	33.6
loc_per_fn_r	9	24.3
loc_per_fn_r_exp	13	30.5
loc_per_fn_r_not_exp	8	22.6
loc_per_fn_src	5	5.0	TRUE
rel_whitespace_R	9	93.1
rel_whitespace_src	16	75.3
rel_whitespace_vignettes	7	88.3
rel_whitespace_tests	18	98.2	TRUE
doclines_per_fn_exp	92	89.0
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	1395	98.6	TRUE

---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package (not linked here).

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
2270953078	R-CMD-check	skipped	f731dd	106	2022-05-04

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following error:

1. Error in stopifnot(no("func") || is.function(func), no("func") || is.list(args), :
   object 'cmdargs' not found

R CMD check generated the following check_fail:

1. no_description_depends

Test coverage with covr

ERROR: Test Coverage Failed

Cyclocomplexity with cyclocomp

Error : Build failed, unknown error, standard output:
�[33m* checking for file ‘lme4/DESCRIPTION’ ... OK

• preparing ‘lme4’:
• checking DESCRIPTION meta-information ... OK
• cleaning src
• installing the package to process help pages
  -----------------------------------
  ERROR: dependencies ‘minqa’, ‘nloptr’, ‘statmod’, ‘RcppEigen’ are not available for package ‘lme4’
• removing ‘/tmp/RtmpqbvYXS/Rinst140584d7deafd/lme4’
  -----------------------------------
  ERROR: package installation failed
  �[39m

Static code analyses with lintr

lintr found the following 1222 potential issues:

message	number of times
Avoid 1:length(...) expressions, use seq_len.	2
Avoid 1:ncol(...) expressions, use seq_len.	1
Avoid 1:nrow(...) expressions, use seq_len.	4
Avoid attach/detach, it is easy to create errors with it	8
Avoid length(...):1 expressions, use seq_len.	1
Avoid library() and require() calls in packages	6
Avoid trailing semicolons, they are not needed.	3
Avoid using sapply, consider vapply instead, that's type safe	64
Lines should not be more than 80 characters.	1127
Use <-, not =, for assignment.	6

---

4. Other Checks

Details of other checks (click to open)

✖️ The following 13 function names are duplicated in other packages:

• • checkConv from AICcmodavg
• • checkConv from gmm
• • checkConv from meboot
• • dummy from AggregateR
• • dummy from BAT
• • dummy from BETS
• • dummy from dummy
• • dummy from expss
• • dummy from hablar
• • dummy from OrdFacReg
• • dummy from rigr
• • dummy from RVAideMemoire
• • dummy from tidyft
• • dummy from vannstats
• • dummy from wakefield
• • factorize from admisc
• • factorize from conf.design
• • factorize from elliptic
• • factorize from Epi
• • factorize from gmp
• • factorize from labdsv
• • factorize from mosaic
• • factorize from QCApro
• • factorize from RcmdrPlugin.KMggplot2
• • factorize from rminer
• • factorize from sfsmisc
• • getL from ctgt
• • getL from sitar
• • getL from VCA
• • golden from psycho
• • isSingular from dataMaid
• • isSingular from dataReporter
• • isSingular from rrcov
• • lmer from lmerTest
• • lmer from mixlm
• • lmList from nlme
• • mkRespMod from MatrixModels
• • ngrps from brms
• • refit from bartCause
• • refit from fido
• • refit from fxregime
• • refit from gamlss
• • refit from genscore
• • refit from lmSubsets
• • refit from modeltools
• • refit from pulsar
• • refit from randomLCA
• • refit from simex
• • rePCA from Momocs
• • sdcor2cov from SIN

---

Package Versions

package	version
pkgstats	0.0.4.53
pkgcheck	0.0.3.29

[mpadge]

@maelle Opinions and insights requested, please 😄. This will automatically go live the next time the system is rebuit (weekly, Monday night). Do you think that's okay? It will likely be the first check that may need to be ignored, because duplicate fn names might not be such an issue for truly unrelated packages. Then again, I've already discovered some in my packages which it would be good to rectify, so it's already helped me!

---

Update: I just realised that it will be much better to group all packages in the above output into one line, so there are only 13 lines in total. I'll do that now.

[mpadge]

4. Other Checks

Details of other checks (click to open)

✖️ The following 13 function names are duplicated in other packages:

• • checkConv from AICcmodavg, gmm, meboot
• • dummy from AggregateR, BAT, BETS, dummy, expss, hablar, OrdFacReg, rigr, RVAideMemoire, tidyft, vannstats, wakefield
• • factorize from admisc, conf.design, elliptic, Epi, gmp, labdsv, mosaic, QCApro, RcmdrPlugin.KMggplot2, rminer, sfsmisc
• • getL from ctgt, sitar, VCA
• • golden from psycho
• • isSingular from dataMaid, dataReporter, rrcov
• • lmer from lmerTest, mixlm
• • lmList from nlme
• • mkRespMod from MatrixModels
• • ngrps from brms
• • refit from bartCause, fido, fxregime, gamlss, genscore, lmSubsets, modeltools, pulsar, randomLCA, simex
• • rePCA from Momocs
• • sdcor2cov from SIN

---

[e-kotov]

@mpadge , would it be possible to run pkgstats::pkgstats_fn_names() or a similar user facing function to check for uniqueness of a function name passed as just a string?

Currently, the process is: 1. I develop a function -> 2. I commit and push it to GitHub -> 3. GitHub action runs and does all other checks, which takes several minutes. -> 4. I eyeball the report looking for details of which function names might have clashes. I could have done that locally, but that is also a bit of a bother to setup ctags.

And all of this just just to learn that my function name is a dupe in some other package.

Ideally, I would know that before I gave the function a name, committed it to repo and waited for the checks. So just having a quick helper that would allow to check a potential function name in the pkgstats database would be very handy and would save a lot of dev time, and also a lot of compute.

[mpadge]

Great idea @e-kotov, I'll re-open and implement straight away.