readxl is not able to read an xls file

[smsaladi]

I have an excel file that's generated by an application that reads data off an instrument. It looks like read_excel is not able to successfully parse excel files exported by the application, returning just an empty tibble:

library(readxl)
data <- read_xls("2020-06-02_02-39-48_Quantitation_Summary.xls")
#> data                                                                                                             
## A tibble: 0 x 0

In case it's helpful, it looks like pandas is able to process it ok, but with an warning:

In [3]: df = pd.read_excel("2020-06-02_02-39-48_Quantitation_Summary.xls")
WARNING *** file size (8461) not 512 + multiple of sector size (512)

In [4]: df.head()
Out[4]:
   Unnamed: 0 Well Fluor  Content Sample        C(t)  SQ
0         NaN  A03  SYBR  Unkn-01    H2O   62.048927 NaN
1         NaN  A04  SYBR  Unkn-05    H2O   68.577469 NaN
2         NaN  A09  SYBR   NTC-09    H2O   60.147350 NaN
3         NaN  A10  SYBR   NTC-13    H2O   85.389522 NaN
4         NaN  B03  SYBR  Unkn-02    CVS  106.360012 NaN

Github doesn't like .xls files attached, so I zipped it up:
2020-06-02_02-39-48_Quantitation_Summary.xls.zip

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] reprex_0.3.0    readxl_1.3.1    cowplot_1.0.0   forcats_0.4.0   stringr_1.4.0   dplyr_0.8.3     purrr_0.3.3    
 [8] readr_1.3.1     tidyr_1.0.0     tibble_2.1.3    ggplot2_3.3.0   tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5 xfun_0.12        haven_2.2.0      lattice_0.20-38  colorspace_1.4-1 vctrs_0.2.1     
 [7] generics_0.0.2   htmltools_0.4.0  yaml_2.2.0       base64enc_0.1-3  rlang_0.4.2      pillar_1.4.3    
[13] withr_2.1.2      glue_1.3.1       DBI_1.1.0        dbplyr_1.4.2     modelr_0.1.5     lifecycle_0.1.0 
[19] munsell_0.5.0    gtable_0.3.0     cellranger_1.1.0 rvest_0.3.5      evaluate_0.14    knitr_1.27      
[25] callr_3.4.0      ps_1.3.0         fansi_0.4.1      broom_0.5.3      Rcpp_1.0.3       clipr_0.7.0     
[31] backports_1.1.5  scales_1.1.0     jsonlite_1.6     fs_1.3.1         hms_0.5.3        digest_0.6.23   
[37] stringi_1.4.5    processx_3.4.1   grid_3.6.1       cli_2.0.1        tools_3.6.1      magrittr_1.5    
[43] whisker_0.4      crayon_1.3.4     pkgconfig_2.0.3  zeallot_0.1.0    xml2_1.2.2       lubridate_1.7.4 
[49] assertthat_0.2.1 rmarkdown_2.0    httr_1.4.1       rstudioapi_0.10  R6_2.4.1         nlme_3.1-143    
[55] compiler_3.6.1

[smsaladi]

Looks like this is an issue with libxls not being able to parse this file. I've opened up an issue there: libxls/libxls#76

[jennybc]

As expected, now I've pulled in the most recent libxls, this now works 🎉
Note that this currently applies only to the dev version of readxl.

library(readxl)

data <- read_xls("investigations/2020-06-02_02-39-48_Quantitation_Summary.xls")
data
#> # A tibble: 32 x 6
#>    Well  Fluor Content Sample `C(t)` SQ   
#>    <chr> <chr> <chr>   <chr>   <dbl> <lgl>
#>  1 A03   SYBR  Unkn-01 H2O      62.0 NA   
#>  2 A04   SYBR  Unkn-05 H2O      68.6 NA   
#>  3 A09   SYBR  NTC-09  H2O      60.1 NA   
#>  4 A10   SYBR  NTC-13  H2O      85.4 NA   
#>  5 B03   SYBR  Unkn-02 CVS     106.  NA   
#>  6 B04   SYBR  Unkn-06 CVS      48.7 NA   
#>  7 B09   SYBR  NTC-10  CVS      63.5 NA   
#>  8 B10   SYBR  NTC-14  CVS      82.7 NA   
#>  9 C03   SYBR  Unkn-03 QTIP     69.8 NA   
#> 10 C04   SYBR  Unkn-07 QTIP     73.2 NA   
#> # … with 22 more rows

^{Created on 2021-07-29 by the reprex package (v2.0.0.9000)}