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zachcp/devtools_check.log

Created January 20, 2020 17:49
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rCDK build failure 20200120
Raw
devtools_check.log
* using log directory ‘/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck’
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘rcdk/DESCRIPTION’ ... OK
* this is package ‘rcdk’ version ‘3.4.9.2’
* 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 serialization versions ... OK
* checking whether package ‘rcdk’ can be installed ... OK
* checking installed package size ... 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 ... 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 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 ... OK
* checking Rd files ... 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 documentation object 'copy.image.to.clipboard'
‘molecule’ ‘depictor’
Undocumented arguments in documentation object 'eval.atomic.desc'
‘molecule’ ‘which.desc’ ‘verbose’
Undocumented arguments in documentation object 'eval.desc'
‘molecules’ ‘which.desc’ ‘verbose’
Undocumented arguments in documentation object 'generate.formula'
‘mass’ ‘window’ ‘elements’ ‘validation’ ‘charge’
Undocumented arguments in documentation object 'generate.formula.iter'
‘mass’ ‘window’ ‘elements’ ‘validation’ ‘charge’ ‘as.string’
Undocumented arguments in documentation object 'get.alogp'
‘molecule’
Undocumented arguments in documentation object 'get.atomic.desc.names'
‘type’
Undocumented arguments in documentation object 'get.desc.names'
‘type’
Undocumented arguments in documentation object 'get.formula'
‘mf’ ‘charge’
Undocumented arguments in documentation object 'get.isotopes.pattern'
‘formula’ ‘minAbund’
Undocumented arguments in documentation object 'get.mcs'
‘mol1’ ‘mol2’ ‘as.molecule’
Undocumented arguments in documentation object 'get.mol2formula'
‘molecule’ ‘charge’
Undocumented arguments in documentation object 'get.tpsa'
‘molecule’
Undocumented arguments in documentation object 'get.volume'
‘molecule’
Undocumented arguments in documentation object 'get.xlogp'
‘molecule’
Undocumented arguments in documentation object 'isvalid.formula'
‘formula’ ‘rule’
Undocumented arguments in documentation object 'matches'
‘query’ ‘target’ ‘return.matches’
Undocumented arguments in documentation object 'set.charge.formula'
‘formula’ ‘charge’
Undocumented arguments in documentation object 'view.image.2d'
‘molecule’ ‘depictor’
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
--- re-building ‘molform.Rmd’ using rmarkdown
--- finished re-building ‘molform.Rmd’
--- re-building ‘using-rcdk.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
rcdk
--- call from context ---
eval.desc(mols, descNames)
--- call from argument ---
length(vals) == 1 && is.na(vals)
--- R stacktrace ---
where 1: eval.desc(mols, descNames)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::.buildOneVignette("using-rcdk.Rmd", "/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck/vign_test/rcdk",
TRUE, FALSE, "using-rcdk", "UTF-8", "/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T//RtmpgsaTPM/filef1d06a9d83ea.rds")
--- value of length: 277 type: logical ---
do.call..rbind...vals.
C(Br)(Cl)(Cl)Cl FALSE
ClC(F)(F)F FALSE
C(Cl)(Cl)(Cl)Cl FALSE
C(F)(F)(F)F FALSE
BrC(Br)Br FALSE
C(Cl)(F)F FALSE
C(Cl)(Cl)F FALSE
C(Cl)(Cl)Cl FALSE
C(F)(F)F FALSE
C(Br)Br FALSE
C(Cl)Cl FALSE
C(F)F FALSE
C(I)I FALSE
O=C FALSE
C(=O)O FALSE
CBr FALSE
CCl FALSE
CF FALSE
CI FALSE
CO FALSE
CS FALSE
C(C(F)(F)F)(Cl)(Cl)F FALSE
C(C(F)(F)F)(F)(F)F FALSE
C(C(Cl)Cl)(F)(F)F FALSE
C(=C(Cl)Cl)Cl FALSE
C(C=O)(Cl)(Cl)Cl FALSE
C(C(Cl)(Cl)Cl)(Cl)Cl FALSE
C(C(F)(F)F)(F)F FALSE
C(C(Br)Br)(Br)Br FALSE
C(CCl)(Cl)(Cl)Cl FALSE
C(C(Cl)Cl)(Cl)Cl FALSE
C=C(F)F FALSE
C(C(F)F)(F)F FALSE
C=CBr FALSE
CC(=O)Cl FALSE
CC(Cl)(Cl)Cl FALSE
C(CCl)(Cl)Cl FALSE
C=CF FALSE
CC(F)(F)F FALSE
CC(Br)Br FALSE
C(CBr)Br FALSE
C(C)(Cl)Cl FALSE
C(CCl)Cl FALSE
CC(F)F FALSE
C(CF)F FALSE
CC(=O)O FALSE
COC=O FALSE
CCBr FALSE
CCCl FALSE
CCF FALSE
CCI FALSE
COC FALSE
CCO FALSE
OCCO FALSE
CSC FALSE
CCS FALSE
CSSC FALSE
SCCS FALSE
CC(=C)Cl FALSE
C(C(CCl)Cl)Cl FALSE
C(C(C)Cl)Cl FALSE
CC(=O)C FALSE
CCC=O FALSE
CC1CO1 FALSE
CCOC=O FALSE
CC(=O)OC FALSE
CCC(=O)O FALSE
C(CC)Br FALSE
CC(C)Cl FALSE
CCCCl FALSE
CC(C)I FALSE
CCCI FALSE
CC(C)O FALSE
CCOC FALSE
CCCO FALSE
CC(O)CO FALSE
C(CCO)O FALSE
CC(C)S FALSE
CCCS FALSE
c1ccco1 FALSE
c1cccs1 FALSE
C1C=CCO1 FALSE
CC(=C)C(=O)O FALSE
C(C(CC)Cl)Cl FALSE
CC(C(C)Cl)Cl FALSE
C(=O)CCC FALSE
CCC(=O)C FALSE
CC(C)C=O FALSE
O1CCCC1 FALSE
CCCC(=O)O FALSE
CCOC(=O)C FALSE
CC(C)C(=O)O FALSE
COC(=O)CC FALSE
CCCOC=O FALSE
S1CCCC1 FALSE
C(CCC)Br FALSE
CC(CC)Br FALSE
CCCCCl FALSE
CC(CC)Cl FALSE
CC(C)(C)Cl FALSE
CC(C)CCl FALSE
CCCCO FALSE
CC(CC)O FALSE
CCOCC FALSE
C(C(C)C)O FALSE
CC(C)(C)O FALSE
CCCOC FALSE
OCCC(C)O FALSE
OCCCCO FALSE
CC(O)C(O)C FALSE
C(C(CO)C)O FALSE
CCCCS FALSE
CCC(S)C FALSE
CC(C)(C)S FALSE
CC(C)CS FALSE
CSCCC FALSE
c1cc(sc1)C FALSE
CC(C)C(=O)C FALSE
CCCCC=O FALSE
CCCC(=O)C FALSE
CCC(=O)CC FALSE
CCCCOC=O FALSE
CC(CC)OC=O FALSE
CC(C)(C)OC=O FALSE
CCOC(=O)CC FALSE
CC(C)COC=O FALSE
CC(=O)OC(C)C FALSE
CCCC(=O)OC FALSE
CC(C)CC(=O)O FALSE
CC(C)(C)C(=O)O FALSE
CCCCC(=O)O FALSE
CCCOC(=O)C FALSE
CCCCCCl FALSE
C(C(C)(C)C)O FALSE
CCOC(C)C FALSE
CCOCCC FALSE
C(C(CC)C)O FALSE
CC(CC)(C)O FALSE
C(CC(C)C)O FALSE
CC(C(C)C)O FALSE
CCCCOC FALSE
CCC(C)OC FALSE
CC(C)(C)OC FALSE
C(CCCC)O FALSE
CC(CCC)O FALSE
CCC(CC)O FALSE
OCCCCCO FALSE
CSCCCC FALSE
CSC(C)(C)C FALSE
CCCCCS FALSE
c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)Cl FALSE
c1(c(c(c(c(c1F)F)F)F)F)F FALSE
c1cc(c(cc1Cl)Cl)Cl FALSE
c1c(cccc1Cl)Cl FALSE
c1(ccccc1Cl)Cl FALSE
c1(ccc(cc1)Cl)Cl FALSE
c1ccc(cc1O)Cl FALSE
c1cccc(c1O)Cl FALSE
c1cc(ccc1O)Cl FALSE
c1(ccccc1)O FALSE
c1(ccccc1O)O FALSE
c1(cccc(c1)O)O FALSE
c1cc(ccc1O)O FALSE
C1CCC(=O)CC1 FALSE
CC(=O)CC(=O)OCC FALSE
CCOC(=O)C(=O)OCC FALSE
C1CCC(CC1)O FALSE
CC(=O)C(C)(C)C FALSE
CC(C)C(=O)CC FALSE
CCCCCC=O FALSE
CC(=O)CCCC FALSE
CCC(=O)CCC FALSE
CC(=O)CC(C)C FALSE
CC(=O)C(C)CC FALSE
CC(=O)OCCCC FALSE
CC(=O)OC(C)CC FALSE
CC(=O)OC(C)(C)C FALSE
CCCC(=O)OCC FALSE
CCC(CC)C(=O)O FALSE
CCOC(=O)C(C)C FALSE
CCCCCC(=O)O FALSE
CC(=O)OCC(C)C FALSE
CCCCCOC=O FALSE
CCCOC(=O)CC FALSE
CCOCCCC FALSE
CCOC(C)(C)C FALSE
CC(C)OC(C)C FALSE
CCC(CC)CO FALSE
CCCCCCO FALSE
CC(CCCC)O FALSE
C(C(CCC)C)O FALSE
CC(CC(C)C)O FALSE
CCCCCOC FALSE
OCCCCCCO FALSE
CC(CC(C)O)(C)O FALSE
CCCSCCC FALSE
CCSC(C)(C)C FALSE
CCCCCCS FALSE
CCCSSCCC FALSE
c1ccccc1C(Cl)(Cl)Cl FALSE
c1(ccccc1)C(Cl)Cl FALSE
c1ccccc1C(=O)O FALSE
c1cc(ccc1O)C=O FALSE
c1(ccccc1O)C=O FALSE
c1ccccc1CCl FALSE
c1(ccccc1)CO FALSE
c1ccc(cc1O)C FALSE
c1cccc(c1O)C FALSE
c1cc(ccc1O)C FALSE
CCOC(=O)CC(=O)OCC FALSE
CC(C)C(=O)C(C)C FALSE
CCCCCCC=O FALSE
CC(=O)CCCCC FALSE
CCCC(=O)CCC FALSE
C1(CCCCC1)(C)O FALSE
CC(=O)CCC(C)C FALSE
CCCCOC(=O)CC FALSE
CC(C)CC(=O)OCC FALSE
CCCCCCC(=O)O FALSE
CCCCCCOC=O FALSE
CCCC(=O)OCCC FALSE
CCCCCCCO FALSE
CC(CCCCC)O FALSE
C(CCCC(C)C)O FALSE
CCCCCCCS FALSE
c1cc(c(cc1C=O)OC)O FALSE
c1cc(ccc1CC)O FALSE
c1(c(cccc1C)O)C FALSE
c1cc(cc(c1O)C)C FALSE
c1c(ccc(c1O)C)C FALSE
c1c(c(c(cc1)C)O)C FALSE
c1(cc(ccc1C)O)C FALSE
c1c(cc(cc1O)C)C FALSE
CCOC(=O)C=CC(=O)OCC FALSE
CCCCCCCC=O FALSE
CCCCCCC(=O)C FALSE
CCCCOC(=O)CCC FALSE
CCCCCCCOC=O FALSE
CCCCCCOC(=O)C FALSE
CC(C)COC(=O)C(C)C FALSE
CCC(C)OC(C)CC FALSE
C(C(CCCC)CC)O FALSE
C(CCCCCCC)O FALSE
CC(CCCCCC)O FALSE
CCCCCCCCS FALSE
c1(ccccc1)C(=O)OCC FALSE
c1cccc(c1)COCC FALSE
C1(CC(=O)C=C(C1)C)(C)C FALSE
CC(C)CC(=O)CC(C)C FALSE
CCCCCCCC(=O)C FALSE
CCCCC(=O)CCCC FALSE
CCCCCCCOC(=O)C FALSE
CCCCCCCCC(=O)O FALSE
CCCCCCCCOC=O FALSE
CC(C)CC(CC(C)C)O FALSE
CCCCCCCCCO FALSE
CCCCCCCC(C)O FALSE
CCCCCCCCCS FALSE
c1cccc(c1C(=O)OC)C(=O)OC FALSE
CC=Cc1ccc(cc1)OC FALSE
c1(ccc(cc1)C(C)(C)C)O FALSE
CCCCCCCCCC(=O)O FALSE
CC(C)CCOC(=O)CC(C)C FALSE
CCCCCCCCOC(=O)C FALSE
CCCCCCCCCCO FALSE
CCCCCCCCCCS FALSE
C=CC(=O)OCC(CCCC)CC FALSE
CCCCCCCCCCC(=O)O FALSE
CCCCCCCCCC(=O)OC FALSE
CCCCCCCCCCCO FALSE
c1cccc(c1C(=O)OCC)C(=O)OCC FALSE
CCCCCCCCCCOC(=O)C FALSE
CCCCCCCCCCCC(=O)O FALSE
CCCCCCOCCCCCC FALSE
CCCCCCCCCCCCC(=O)O FALSE
c1cccc2c1C(=O)c3c(cccc3)C2=O FALSE
c1cc(ccc1C(C)(C)CC(C)(C)C)O FALSE
--- function from context ---
function (molecules, which.desc, verbose = FALSE)
{
if (class(molecules) != "list") {
jclassAttr <- attr(molecules, "jclass")
if (jclassAttr != "org/openscience/cdk/interfaces/IAtomContainer") {
stop("Must provide a list of molecule objects or a single molecule object")
}
molecules <- list(molecules)
}
else {
jclassAttr <- lapply(molecules, attr, "jclass")
if (any(jclassAttr != "org/openscience/cdk/interfaces/IAtomContainer")) {
stop("molecule must be an IAtomContainer")
}
}
dcob <- get.chem.object.builder()
if (length(which.desc) == 1) {
desc <- .jnew(which.desc)
.jcall(desc, "V", "initialise", dcob)
dnames <- .jcall(desc, "[Ljava/lang/String;", "getDescriptorNames")
dnames <- gsub("-", ".", dnames)
descvals <- lapply(molecules, function(a, b) {
val <- tryCatch({
.jcall(b, "Lorg/openscience/cdk/qsar/DescriptorValue;",
"calculate", a)
}, warning = function(e) return(NA), error = function(e) return(NA))
}, b = desc)
vals <- lapply(descvals, .get.desc.values, nexpected = length(dnames))
vals <- data.frame(do.call("rbind", vals))
names(vals) <- dnames
return(vals)
}
else {
counter <- 1
dl <- list()
dnames <- c()
for (desc in which.desc) {
if (verbose) {
cat("Processing ", gsub("org.openscience.cdk.qsar.descriptors.molecular.",
"", desc), "\n")
}
desc <- .jnew(desc)
.jcall(desc, "V", "initialise", dcob)
dnames <- .jcall(desc, "[Ljava/lang/String;", "getDescriptorNames")
dnames <- gsub("-", ".", dnames)
descvals <- lapply(molecules, function(a, check) {
val <- tryCatch({
.jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;",
"calculate", a, check = check)
})
}, check = FALSE)
vals <- lapply(descvals, .get.desc.values, nexpected = length(dnames))
vals <- data.frame(do.call("rbind", vals))
if (length(vals) == 1 && is.na(vals)) {
vals <- as.data.frame(matrix(NA, nrow = 1, ncol = length(dnames)))
}
names(vals) <- dnames
dl[[counter]] <- vals
counter <- counter + 1
}
do.call("cbind", dl)
}
}
<bytecode: 0x7f9999b0eb98>
<environment: namespace:rcdk>
--- function search by body ---
Function eval.desc in namespace rcdk has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
SUMMARY: processing the following file failed:
‘using-rcdk.Rmd’
Error: Vignette re-building failed.
Execution halted
* DONE
Status: 2 WARNINGs
See
‘/private/var/folders/yc/53w8dbxx2hjg11_brr2pj5740000gn/T/RtmpWPpy1T/rcdk.Rcheck/00check.log’
for details.
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