* using log directory ‘/srv/hornik/tmp/CRAN_pretest/pleioh2g.Rcheck’
* using R Under development (unstable) (2025-09-17 r88853)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘pleioh2g/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pleioh2g’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Yujie Zhao <yujiezhao@hsph.harvard.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Heritability (3:34)
  Pleiotropic (3:22)
  heritability (12:61)
  pleiotropic (12:49)

Size of tarball: 56513181 bytes
* 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 ‘pleioh2g’ can be installed ... [3s/3s] WARNING
Found the following significant warnings:
  Note: possible error in 'pleiotropyh2_cor_computing_single_prune(target_num, ': unused argument (seed) 
  Note: possible error in 'pleiotropyh2_cor_computing_single(target_num, ': unused argument (seed) 
See ‘/srv/hornik/tmp/CRAN_pretest/pleioh2g.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 code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] NOTE
Cal_rg_h2g_alltraits : <anonymous>: no visible binding for global
  variable ‘N’
Cal_rg_h2g_alltraits: no visible global function definition for
  ‘setNames’
Cal_rg_h2g_jk_alltraits : <anonymous>: no visible binding for global
  variable ‘N’
Cal_rg_h2g_jk_alltraits: no visible global function definition for
  ‘setNames’
generate_proposal_sample_changea_cor: no visible global function
  definition for ‘cov’
h2_liability: no visible global function definition for ‘dnorm’
h2_liability: no visible global function definition for ‘qnorm’
ldsc_h2: no visible global function definition for ‘median’
ldsc_h2: no visible global function definition for ‘qchisq’
ldsc_h2: no visible global function definition for ‘tibble’
ldsc_h2: no visible global function definition for ‘pnorm’
ldsc_h2: no visible binding for global variable ‘h2_Z’
ldsc_rg: no visible global function definition for ‘cli_alert_warning’
ldsc_rg: no visible global function definition for ‘median’
ldsc_rg: no visible global function definition for ‘qchisq’
ldsc_rg: no visible global function definition for ‘pnorm’
ldsc_rg: no visible binding for global variable ‘h2_Z’
ldsc_rg: no visible global function definition for ‘na.omit’
merge_sumstats: no visible binding for global variable ‘SNP’
merge_sumstats: no visible binding for global variable ‘N’
merge_sumstats: no visible binding for global variable ‘Z’
merge_sumstats: no visible binding for global variable ‘A1’
merge_sumstats: no visible binding for global variable ‘CHR’
merge_sumstats: no visible global function definition for ‘na.omit’
perform_analysis: no visible global function definition for ‘cov’
pleiotropyh2_cor_computing_single: no visible global function
  definition for ‘sd’
pleiotropyh2_cor_computing_single_prune: no visible global function
  definition for ‘sd’
pleiotropyh2_nocor_computing_single: no visible global function
  definition for ‘sd’
pruning_pleioh2g_wrapper : <anonymous> : <anonymous>: possible error in
  pleiotropyh2_cor_computing_single_prune(target_num,
  phenotype_path_update, save_path, h2_vector_update_3,
  h2_vector_mat_update_3, Results_full_rg_update_3,
  Results_full_rg_array_update_3, sample_rep, tolerance, seed): unused
  argument (seed)
pruning_pleioh2g_wrapper : <anonymous> : <anonymous>: no visible
  binding for global variable ‘phenotype_path_update’
pruning_pleioh2g_wrapper : <anonymous> : <anonymous>: no visible
  binding for global variable ‘save_path’
pruning_pleioh2g_wrapper : <anonymous> : <anonymous>: possible error in
  pleiotropyh2_cor_computing_single(target_num, phenotype_path_update,
  save_path, h2_vector_update_3, h2_vector_mat_update_3,
  Results_full_rg_update_3, Results_full_rg_array_update_3, sample_rep,
  tolerance, seed): unused argument (seed)
read_ld: no visible global function definition for ‘ldscore_files’
read_m: no visible global function definition for ‘ldscore_files’
read_sumstats: no visible binding for global variable ‘.x’
read_sumstats: no visible global function definition for ‘na.omit’
read_wld: no visible global function definition for ‘ldscore_files’
Undefined global functions or variables:
  .x A1 CHR N SNP Z cli_alert_warning cov dnorm h2_Z ldscore_files
  median na.omit phenotype_path_update pnorm qchisq qnorm save_path sd
  setNames tibble
Consider adding
  importFrom("stats", "cov", "dnorm", "median", "na.omit", "pnorm",
             "qchisq", "qnorm", "sd", "setNames")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'Cal_rg_h2g_alltraits.Rd':
  \examples lines wider than 100 characters:
     munged_sumstats = list("401.1" = sumstats_munged_example_input(example = "401.1"), "250.2" = sumstats_munged_example_input(example = "2 ... [TRUNCATED]
     results<-Cal_rg_h2g_alltraits(phenotype, munged_sumstats, ld_path, wld_path, sample_prev, population_prev)

Rd file 'Cal_rg_h2g_jk_alltraits.Rd':
  \examples lines wider than 100 characters:
     munged_sumstats = list("401.1" = sumstats_munged_example_input(example = "401.1"), "250.2" = sumstats_munged_example_input(example = "2 ... [TRUNCATED]
     results_jk<-Cal_rg_h2g_jk_alltraits(n_block, hmp3, phenotype, munged_sumstats, ld_path, wld_path, sample_prev, population_prev)

Rd file 'Prune_disease_selection_DTrgzscore.Rd':
  \examples lines wider than 100 characters:
     Rg_prune<-Prune_disease_selection_DTrgzscore(Target_disease, trait_name,Results_full_rg_15D,Rg_mat_z_15D,rg_threshold)

Rd file 'generate_proposal_sample_changea_cor.Rd':
  \examples lines wider than 100 characters:
     generate_proposal_sample_changea_cor(Results_full_rg_15D, Results_full_rg_array_15D, plei_h2_idx, ratio_a,seed)

These lines will be truncated in the PDF manual.
* 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 ... [196s/138s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                                          user system elapsed
pruning_pleioh2g_wrapper                84.284  4.247  60.969
Cal_rg_h2g_jk_alltraits                 60.893  3.274  43.699
Cal_rg_h2g_alltraits                    28.851  2.722  22.425
pleiotropyh2_cor_computing_single_prune  5.940  0.002   5.945
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] OK
  Running ‘testthat.R’ [1s/1s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [5s/5s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: Unicode character ✖ (U+2716)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘pleioh2g-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 5 NOTEs