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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data xcms
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* checking for file ‘xcms/DESCRIPTION’ ... OK
* preparing ‘xcms’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘LC-MS-feature-grouping.Rmd’ using rmarkdown
--- finished re-building ‘LC-MS-feature-grouping.Rmd’

--- re-building ‘xcms-direct-injection.Rmd’ using rmarkdown

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Error: processing vignette 'xcms-direct-injection.Rmd' failed with diagnostics:
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--- failed re-building ‘xcms-direct-injection.Rmd’

--- re-building ‘xcms-lcms-ms.Rmd’ using rmarkdown

Quitting from lines 79-86 [load-dda-data] (xcms-lcms-ms.Rmd)
Error: processing vignette 'xcms-lcms-ms.Rmd' failed with diagnostics:
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--- failed re-building ‘xcms-lcms-ms.Rmd’

--- re-building ‘xcms.Rmd’ using rmarkdown
filterFeatures          package:ProtGenerics           R Documentation

_F_i_l_t_e_r _f_e_a_t_u_r_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Implementations of this generic filter function are supposed to
     filter _features_ in 'object' based on a filter criteria defined
     by parameter 'filter'.

_U_s_a_g_e:

     filterFeatures(object, filter, ...)
     
_A_r_g_u_m_e_n_t_s:

  object: The object to filter.

  filter: The filtering criteria on which 'object' should be filtered.

     ...: Optional parameters.


BlankFlag                 package:xcms                 R Documentation

_F_l_a_g _f_e_a_t_u_r_e_s _b_a_s_e_d _o_n _t_h_e _i_n_t_e_n_s_i_t_y _i_n _b_l_a_n_k _s_a_m_p_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     The `BlankFlag` class and method enable users to flag features of
     an `XcmsExperiment` or `SummarizedExperiment` object based on the
     relationship between the intensity of a feature in blanks compared
     to the intensity in the samples.

     This class and method are part of the possible dispatch of the
     generic function `filterFeatures`. Features *below* (`<`) the
     user-input threshold will be flagged by calling the
     `filterFeatures` function. This means that an extra column will be
     created in `featureDefinitions` or `rowData` called
     `possible_contaminants` with a logical value for each feature.

_U_s_a_g_e:

     BlankFlag(
       threshold = 2,
       blankIndex = integer(),
       qcIndex = integer(),
       na.rm = TRUE
     )
     
     ## S4 method for signature 'XcmsResult,BlankFlag'
     filterFeatures(object, filter, ...)
     
     ## S4 method for signature 'SummarizedExperiment,BlankFlag'
     filterFeatures(object, filter, assay = 1)
     
_A_r_g_u_m_e_n_t_s:

threshold: `numeric` indicates the minimum difference required between
          the mean abundance of a feature in samples compared to the
          mean abundance of the same feature in blanks for it to not be
          considered a possible contaminant. For example, the default
          threshold of 2 signifies that the mean abundance of the
          features in samples has to be at least twice the mean
          abundance in blanks for it to not be flagged as a possible
          contaminant.

blankIndex: `integer` (or `logical`) vector corresponding to the
          indices of blank samples.

 qcIndex: `integer` (or `logical`) vector corresponding to the indices
          of quality control (QC) samples.

   na.rm: `logical` indicates whether missing values (`NA`) should be
          removed prior to the calculations.

  object: 'XcmsExperiment' or 'SummarizedExperiment'. For an
          'XcmsExperiment' object, the 'featureValues(object)' will be
          evaluated, and for 'Summarizedesxperiment' the 'assay(object,
          assay)'. The object will be filtered.

  filter: The parameter object selecting and configuring the type of
          filtering. It can be one of the following classes:
          'RsdFilter', 'DratioFilter', 'PercentMissingFilter' or
          'BlankFlag'.

     ...: Optional parameters. For 'object' being an 'XcmsExperiment':
          parameters for the 'featureValues()' call.

   assay: For filtering of 'SummarizedExperiment' objects only.
          Indicates which assay the filtering will be based on. Note
          that the features for the entire object will be removed, but
          the computations are performed on a single assay. Default is
          1, which means the first assay of the 'object' will be
          evaluated.

_V_a_l_u_e:

     For `BlankFlag`: a `BlankFlag` class. `filterFeatures` returns the
     input object with an added column in the features metadata called
     `possible_contaminants` with a logical value for each feature.
     This is added to `featureDefinitions` for `XcmsExperiment` objects
     and `rowData` for `SummarizedExperiment` objects.

_A_u_t_h_o_r(_s):

     Philippine Louail

_S_e_e _A_l_s_o:

     Other Filter features in xcms: 'DratioFilter',
     'PercentMissingFilter', 'RsdFilter'


--- finished re-building ‘xcms.Rmd’

SUMMARY: processing the following files failed:
  ‘xcms-direct-injection.Rmd’ ‘xcms-lcms-ms.Rmd’

Error: Vignette re-building failed.
Execution halted