* using log directory ‘/srv/hornik/tmp/CRAN/MicrobiomeSurv.Rcheck’
* using R Under development (unstable) (2023-09-26 r85226)
* 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 ‘MicrobiomeSurv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiomeSurv’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Thi Huyen Nguyen <thihuyen.nguyen@uhasselt.be>’

New submission

Possibly misspelled words in DESCRIPTION:
  Microbiome (4:35)
  SPLS (14:113)
  microbiome (11:38, 11:97, 12:113, 13:76, 16:128)
* 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 ‘MicrobiomeSurv’ can be installed ... [3s/3s] WARNING
Found the following significant warnings:
  Note: possible error in 'try(Temp = Lasoelascox(Survival = Survival[ind.s[i, ': unused argument (Temp = Lasoelascox(Survival = Survival[ind.s[i, ]], Censor = Censor[ind.s[i, ]], Micro.mat[, ind.mi[i, ]], Prognostic = data.frame(perPrognostic), Plots = FALSE, Mean = TRUE, Quantile = Quantile, Standardize = TRUE, Alpha = 1, Fold = 4, nlambda = 100)) 
  Warning: /srv/hornik/tmp/CRAN/MicrobiomeSurv.Rcheck/00_pkg_src/MicrobiomeSurv/man/CVLasoelascox.Rd:45: unexpected '}', expecting '{'
See ‘/srv/hornik/tmp/CRAN/MicrobiomeSurv.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘pls’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] NOTE
CVLasoelascox: no visible global function definition for ‘coef’
CVMSpecificCoxPh: no visible global function definition for ‘p.adjust’
CVMSpecificCoxPh: no visible global function definition for ‘new’
CVMajorityvotes: no visible global function definition for ‘p.adjust’
CVMajorityvotes: no visible binding for global variable ‘quantile’
CVMajorityvotes: no visible global function definition for ‘new’
CVPcaPls: no visible global function definition for ‘p.adjust’
CVPcaPls: no visible global function definition for ‘median’
CVPcaPls: no visible global function definition for ‘new’
CVSITaxa: no visible global function definition for ‘new’
CoxPHUni: no visible global function definition for ‘p.adjust’
DistHR: no visible global function definition for ‘p.adjust’
DistHR: no visible binding for global variable ‘Method’
DistHR: possible error in try(Temp = Lasoelascox(Survival =
  Survival[ind.s[i, ]], Censor = Censor[ind.s[i, ]], Micro.mat[,
  ind.mi[i, ]], Prognostic = data.frame(perPrognostic), Plots = FALSE,
  Mean = TRUE, Quantile = Quantile, Standardize = TRUE, Alpha = 1, Fold
  = 4, nlambda = 100), silent = TRUE): unused argument (Temp =
  Lasoelascox(Survival = Survival[ind.s[i, ]], Censor = Censor[ind.s[i,
  ]], Micro.mat[, ind.mi[i, ]], Prognostic = data.frame(perPrognostic),
  Plots = FALSE, Mean = TRUE, Quantile = Quantile, Standardize = TRUE,
  Alpha = 1, Fold = 4, nlambda = 100))
DistHR: no visible global function definition for ‘new’
Lasoelascox: no visible global function definition for ‘quantile’
Lasoelascox: no visible global function definition for ‘coef’
Lasoelascox: no visible global function definition for ‘par’
Lasoelascox: no visible global function definition for ‘lines’
Lasoelascox: no visible global function definition for ‘abline’
MSpecificCoxPh: no visible global function definition for ‘p.adjust’
MSpecificCoxPh: no visible global function definition for ‘new’
Majorityvotes: no visible global function definition for ‘par’
Majorityvotes: no visible global function definition for ‘points’
Majorityvotes: no visible global function definition for ‘axis’
Majorityvotes: no visible global function definition for ‘box’
Majorityvotes: no visible global function definition for ‘legend’
MiFreq: no visible global function definition for ‘barplot’
MiFreq: no visible global function definition for ‘rainbow’
QuantileAnalysis: no visible global function definition for ‘p.adjust’
QuantileAnalysis: no visible global function definition for ‘axis’
SITaxa: no visible global function definition for ‘p.adjust’
SummaryData: no visible global function definition for ‘across’
SurvPcaClass: no visible global function definition for ‘p.adjust’
SurvPlsClass: no visible global function definition for ‘p.adjust’
ZerosPerGroup: no visible binding for global variable ‘n’
ZerosPerGroup: no visible binding for global variable ‘pp’
ZerosPerGroup: no visible binding for global variable ‘Treatment’
f.pca: no visible global function definition for ‘princomp’
plot,cvle-missing: no visible global function definition for ‘hasArg’
plot,cvle-missing: no visible binding for global variable ‘boxplot’
plot,cvmm-ANY: no visible global function definition for ‘hasArg’
plot,cvmm-ANY: no visible binding for global variable ‘boxplot’
plot,cvmv-ANY: no visible global function definition for ‘hasArg’
plot,cvmv-ANY: no visible global function definition for ‘par’
plot,cvmv-ANY: no visible global function definition for ‘lines’
plot,cvmv-ANY: no visible global function definition for ‘abline’
plot,cvmv-ANY: no visible binding for global variable ‘boxplot’
plot,cvpp-missing: no visible global function definition for ‘hasArg’
plot,cvpp-missing: no visible binding for global variable ‘boxplot’
plot,cvsit-missing: no visible global function definition for ‘hasArg’
plot,cvsit-missing: no visible binding for global variable ‘boxplot’
plot,ms-ANY: no visible global function definition for ‘qnorm’
plot,ms-ANY: no visible global function definition for ‘par’
plot,ms-ANY: no visible global function definition for ‘barplot’
plot,ms-ANY: no visible global function definition for ‘rainbow’
plot,ms-ANY: no visible global function definition for ‘arrows’
plot,ms-ANY: no visible global function definition for ‘abline’
plot,perm-ANY: no visible global function definition for ‘na.exclude’
plot,perm-ANY: no visible global function definition for ‘hasArg’
plot,perm-ANY: no visible global function definition for ‘density’
plot,perm-ANY: no visible global function definition for ‘abline’
plot,perm-ANY: no visible global function definition for ‘quantile’
plot,perm-ANY: no visible global function definition for ‘median’
summary,cvle: no visible global function definition for ‘quantile’
summary,cvmm: no visible global function definition for ‘median’
summary,cvmm: no visible global function definition for ‘quantile’
summary,cvmv: no visible global function definition for ‘quantile’
summary,cvpp: no visible global function definition for ‘quantile’
summary,cvsit : <anonymous>: no visible global function definition for
  ‘median’
summary,cvsit : <anonymous>: no visible global function definition for
  ‘quantile’
summary,ms: no visible global function definition for ‘qnorm’
summary,perm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  Method Treatment abline across arrows axis barplot box boxplot coef
  density hasArg legend lines median n na.exclude new p.adjust par
  points pp princomp qnorm quantile rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
             "boxplot", "legend", "lines", "par", "points")
  importFrom("methods", "hasArg", "new")
  importFrom("stats", "coef", "density", "median", "na.exclude",
             "p.adjust", "princomp", "qnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found if() conditions comparing class() to string:
File ‘MicrobiomeSurv/R/CVSITaxa.R’: if (class(Object) != "cvmm") ...
File ‘MicrobiomeSurv/R/Majorityvotes.R’: if (class(Result) != "ms") ...
File ‘MicrobiomeSurv/R/MiFreq.R’: if (class(Object) != "cvle") ...
File ‘MicrobiomeSurv/R/cvle-class.R’: if (class(x) != "cvle") ...
File ‘MicrobiomeSurv/R/cvmv-class.R’: if (class(x) != "cvmv") ...
File ‘MicrobiomeSurv/R/cvsit-class.R’: if (class(x) != "cvsit") ...
File ‘MicrobiomeSurv/R/perm-class.R’: if (class(x) != "perm") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... [0s/0s] WARNING
prepare_Rd: ./man/CVLasoelascox.Rd:45: unexpected '}', expecting '{'
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'CVLasoelascox.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'CVMSpecificCoxPh.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'CVMajorityvotes.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'CVPcaPls.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'CVSITaxa.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'CoxPHUni.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'DistHR.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'EstimateHR.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'Lasoelascox.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'MSpecificCoxPh.Rd':
  \examples lines wider than 100 characters:
     surv_fam_shan_w3 = data.frame(cbind(as.numeric(Week3_response$T1Dweek), as.numeric(Week3_response$T1D)))
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'Majorityvotes.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'MiFreq.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'QuantileAnalysis.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'SITaxa.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'SurvPcaClass.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'SurvPlsClass.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")

Rd file 'Top1Uni.Rd':
  \examples lines wider than 100 characters:
     names_fam_shan_trim_w3 = c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")
     summary_fam_shan_w3 = CoxPHUni(Survival = surv_fam_shan_w3$Survival, Censor = surv_fam_shan_w3$Censor,

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Unknown packages ‘Microbiome’, ‘microbiomeSurv’ in Rd xrefs
Missing link or links in documentation object 'EstimateHR.Rd':
  ‘[MicrobiomeSurv]{Lasoelacox}’

Missing link or links in documentation object 'MiFreq.Rd':
  ‘[MicrobiomeSurv]{CVLasoelacox}’

Missing link or links in documentation object 'cvle-class.Rd':
  ‘[MicrobiomeSurv]{CVLasoelacox}’ ‘[MicrobiomeSurv]{Lasoelacox}’

Missing link or links in documentation object 'cvmm-class.Rd':
  ‘[MicrobiomeSurv]{CVMspecificCoxPh}’

Missing link or links in documentation object 'perm-class.Rd':
  ‘[MicrobiomeSurv]{Lasoelacox}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘IntermediatePCA’ ‘IntermediatePLS’ ‘Week3_otu’ ‘Week3_response’
  ‘data_zero_per_group_otu_w3’ ‘f.pca’ ‘fam_info_w3’ ‘fam_shan_trim_w3’
  ‘metadata_taxonomy’
Undocumented data sets:
  ‘Week3_otu’ ‘Week3_response’ ‘data_zero_per_group_otu_w3’
  ‘fam_info_w3’ ‘fam_shan_trim_w3’ ‘metadata_taxonomy’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 5 WARNINGs, 3 NOTEs